The Gopher Tortoise (Gopherus polyphemus) is listed in the State of Florida as a threatened species. It is well known that the microbiota of the host is imperative to health promotion and disease mitigation. The diversity of the gut microbiota of the tortoise has not been extensively surveyed. In this study we examined both the bacterial and fungal diversity in the fecal material of this animal using bacterial tag-encoded flexible-Titanium (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded FLX amplicon pyrosequencing. The most dominant bacterial and fungal phylum in all samples were Bacillota and Ascomycota, respectively. Interestingly, the pathogenic fungi Candida tropicalis was detected in all samples suggesting the tortoise could be a reservoir of zoonotic fungi.
","acknowledgements":"This research was done as part of a High Honors project under the leadership of Matthew Janisin, Executive Vice-President (EVP). We thank Maxwell Banor, Nicole Dutton and Donald Zakutansky for their enthusiastic support of this research. We thank Tricia LaPointe, executive director, and Valerie Wolfrey, curator, at the Peace River Wildlife Center (PRWC). We also thank Kellie Reitzel for placing us in contact with members of the PRWC.
","authors":[{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["methodology","writing_originalDraft","writing_reviewEditing"],"email":"vankonil1@mail.gtc.edu","firstName":"Lauren MK","lastName":"Vankoningsveld","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["conceptualization","fundingAcquisition","writing_originalDraft","writing_reviewEditing"],"email":"mclaughlinr@gtc.edu","firstName":"Richard W.","lastName":"McLaughlin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-4634-7096"},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["investigation","methodology","writing_originalDraft"],"email":"bevisd@gtc.edu","firstName":"Durward L.","lastName":"Bevis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/23c7c1f1b35a42cc575165cc40500866.csv"},"extendedData":[],"funding":"This project was supported by funding provided by Gateway Technical College and by the Gateway Foundation.
","image":{"url":null},"imageCaption":"An analysis of the Predicted Bacterial Phyla (1A), Predicted Bacterial Genera (1B), Bacterial Information (1C), Predicted Fungal Phyla (1D), Predicted Fungal Genera (1E), and Fungal Information (1F). * relative percentage of zero-radius operational taxonomic units (ZOTUs).
","imageTitle":"Bacterial and fungal diversity present in the fecal material of two gopher tortoises.
","methods":"Animals and sample collection
The two gopher tortoises in this study live at the Peace River Wildlife Center Punta Gorda, Florida. Ruffles is a 61-year-old female, with severe metabolic bone disease (MBD) from many years of incorrect husbandry which has resulted in a disfigured shell. The shell length is 9 inches. Legolas is a female of unknown age with a shell length of 14.5 inches. Three samples from each tortoise were collected over an approximate one-month period of time and placed into separate containers. The date of sampling is found in Table 1. All samples were transported and then stored in a − 40 °C freezer until used.
Microbiota analysis
The bacterial diversity and the fungal diversity within the six-gopher tortoise fecal samples used for our study were determined using bTEFAP® services. These assays were performed by MR DNA (Shallowater, TX). Primers 515F-806 and ITS1-2 were used to amplify bacterial and fungal DNA, respectively. A more detailed explanation of the methods can be found in the study by Sanchez et al., 2021.
","reagents":"","patternDescription":"Gopher Tortoises (Gopherus polyphemus) are mostly found in the Southeastern United States and along the Coastal Plains. These animals often burrow in dry sandy environments (Florida Fish and Wildlife Commission, 2025). However, they are subjected to numerous problems including habitat degradation and forced relocation. This can result in an unnatural mixing of the populations and an increased exposure to harmful parasites and disease (Huffman et al., 2018; Cozad et al., 2020; Folt et al., 2022; Whitfield et al., 2024; Jones et al., 2025). Gopher Tortoises are listed as a threatened species by the State of Florida (Florida Fish and Wildlife Commission, 2025).
The diet of many tortoise species generally includes flowers, fruit, legumes, and several varieties of grass. (Abella and Berry, 2016; Figueroa et al., 2024). Though the diet of tortoises is well known, the information regarding the gut microbiome is lacking, which is not uncommon for reptilian herbivores (Sandri et al., 2020). This scarcity of information limits our understanding of the disease process and resilience of the animal.
In this current study amplicon sequencing was performed to obtain an inventory of the bacterial and fungal diversity in the fecal material of two gopher tortoises living at the Peace River Wildlife Center in Punta Gorda Florida. As a noninvasive technique, fecal samples are often utilized to examine the gut microbiome of animals (Tang et al., 2020). Three samples from each tortoise were collected over a one-month period of time. The average number of sequences and ZOTUs for Ruffles’ bacterial diversity was 29429 and 402, respectively. The average number of sequences and ZOTUs for Legolas’ bacterial diversity was 29442 and 410, respectively. The most abundant bacterial phylum in all samples was Bacillota (formerly firmicutes), followed by Pseudomonadota (formerly Proteobacteria). The most predominant genus found in four of the samples was Clostridium (Table 1).
In terms of fungi the average number of sequences and ZOTUs for Ruffles was 28107 and 185, respectively. The average number of sequences and ZOTUs for Legolas was 29200 and 183, respectively. The most abundant fungal phylum throughout the samples was Ascomycota. Candida was the most abundant genera in four of the six samples (Table 1).
Amplicon sequencing has been used to assess the fecal microbiome in different tortoise species. In the Seychelles Giant Tortoises (Aldabrachelys gigantea) living in different environments the most abundant phyla were Bacteroidota (42%), Bacillota (32%), and Spirochaetota (9%) (Sandri et al., 2020). In desert tortoises Bacillota, Bacteroidota, and Actinobacteroidota comprised the majority of the phyla found in the samples (Blair et al., 2025). In captive Bolson Tortoises (Gopherus flavomarginatus) the most abundant phylum was Bacillota followed by Fibrobacterota (García-De La Peña et al., 2019). In a previous study examining the bacterial diversity in the fecal material of a south-central Florida population of gopher tortoises, the most predominant phyla were the Bacillota (36.00%) and Bacteroidetes (36.50%) (Yang et al., 2015). In a more recent study examining a population living in Abacoa Greenway in Jupiter, Florida, 20 different phyla were identified with Bacillota (70.44%) as the most predominant (Giakoumas et al., 2024). In our study, the average percentage of Bacillota for Ruffles was 70.35, and for Legalos was 71.60 which is much higher than detected in the study completed by Yang et al., 2015, but very similar to the results found in the study Giakoumas et al., 2024. Our findings were more consistent with those of previous studies conducted on herbivorous reptiles. For example, in the Galapagos tortoise (Chelonoidis nigra), the green iguana (Iguana iguana), and the marine iguana (Amblyrhynchus cristatus) the relative abundance of Bacillota was 81.10%, 74.00% and 75.10%, respectively (Hong et al., 2011).
In our study, in terms of fungal diversity there were only two phyla present, Ascomycota and Basidiomycota (Table 1). These phyla are dominant in the fecal material of animals, such as Caprinae animals (Lv et al., 2023), swine (Scott et al., 2025), and dogs (Foster et al., 2015). In previous gopher tortoise studies, the fungal diversity was not examined. It has been documented that in the fecal material of reptiles these two phyla are seldomly found (Weber, 1970).
The breakdown of dietary cellulose and hemicellulose, which are major components of plant cell walls, can be accomplished by cellulolytic bacteria. Many such bacteria that are found within the phyla Bacillota as well as Bacteroidetes are capable of cellulose digestion (Bhatia et al., 2024). In addition, aerobic fungi within the phyla Ascomycetes, Basidiomycetes, and Deuteromycetes also contain species which are cellulolytic (McDonald et al., 2012). To the authors knowledge our study is the first to document the fungal diversity in the fecal material of the gopher tortoise. This type of tortoise is a hind-gut-fermenter in which starch is fermented. Unnamed bacterial taxa likely play an important role in the metabolism of the animal and warrant further investigation (Giakoumas et al., 2024). However, this is also likely true of the fungal taxa.
Finally, it is well known animals can be reservoirs for pathogens. In a previous study involving gopher tortoises the potential pathogens Mycoplasmaceae sp., and Helicobacter sp. were detected (Giakoumas et al., 2024). These bacterial species were not detected in this current study. In our study we detected Candida tropicalis with a range of 1.41–75.00% of the sequences for Ruffles and 2.31-92.20% of the sequences for Legolas. This zoonotic fungal species has been detected in the Puff adder (Bitis arietans), the Moroccan cobra (Naja haje legionis) (Ugochukwu et al., 2024), bats (Pinto et al., 2025), cetaceans (Garcia-Bustos et al., 2024), cows (Clarke, 1960), goats, sheep, psittacines, rhea monkeys, horses, sirenians, and shrimp (Cordeiro Rde et al., 2014). This yeast can cause mastitis in cows (Clarke, 1960), blood stream infections in humans (Guinea, 2014) and oropharyngeal candidiasis (Collins et al., 2011).
","references":[{"reference":"Abella SR, Berry KH. 2016. Enhancing and Restoring Habitat for the Desert Tortoise. Journal of Fish and Wildlife Management 7: 255-279.
","pubmedId":"","doi":"10.3996/052015-JFWM-046"},{"reference":"Bhatia T, Bose D, Sharma D, Patel D. 2024. A Review on Cellulose Degrading Microbes and its Applications. Industrial Biotechnology 20: 26-39.
","pubmedId":"","doi":"10.1089/ind.2023.0025"},{"reference":"Blair EM, Margalith NJ, O’Malley MA. 2025. Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota. Microbial Ecology 88: 10.1007/s00248-025-02557-6.
","pubmedId":"","doi":"10.1007/s00248-025-02557-6"},{"reference":"Clarke RTJ. 1960. Rumen Candida species and bovine mastitis. New Zealand Veterinary Journal 8: 79-79.
","pubmedId":"","doi":"10.1080/00480169.1960.33385"},{"reference":"Collins CD, Cookinham S, Smith J. 2011. Management of oropharyngeal candidiasis with localized oral miconazole therapy: efficacy, safety, and patient acceptability. Patient Prefer Adherence 5: 369-74.
","pubmedId":"21845036","doi":"10.2147/PPA.S14047"},{"reference":"Cordeiro Rde A, de Oliveira JS, Castelo-Branco Dde S, Teixeira CE, Marques FJ, Bittencourt PV, et al., Rocha MF. 2015. Candida tropicalis isolates obtained from veterinary sources show resistance to azoles and produce virulence factors. Med Mycol 53(2): 145-52.
","pubmedId":"25550392","doi":""},{"reference":"Cozad RA, Hernandez SM, Norton TM, Tuberville TD, Stacy NI, Stedman NL, Aresco MJ. 2020. Epidemiological Investigation of a Mortality Event in a Translocated Gopher Tortoise (Gopherus polyphemus) Population in Northwest Florida. Front Vet Sci 7: 120.
","pubmedId":"32211432","doi":""},{"reference":"Florida Fish and Wildlife Commission [FFWC] Gopher Tortoise Management Plan. Florida Fish and Wildlife Commission; Tallahassee, FL, USA: 2024. [(accessed on 15 July 2025)]. Available online: https://myfwc.com/media/xd1icqci/gtmgmtplan2024.pdf
","pubmedId":"","doi":""},{"reference":"Figueroa A, Coblentz K, Herrera A, Cuni L, Villate J, Liu H, Araujo MS, Whitfield SM. 2024. Seasonal Frugivory Facilitates Individual Diet Specialization in the Generalist Herbivore Gopher Tortoise. : 10.2139/ssrn.4822385.
","pubmedId":"","doi":"10.2139/ssrn.4822385"},{"reference":"Folt B, Marshall M, Emanuel JA, Dziadzio M, Cooke J, Mena L, et al., McGowan. 2022. Using predictions from multiple anthropogenic threats to estimate future population persistence of an imperiled species. Global Ecology and Conservation 36: e02143.
","pubmedId":"","doi":"10.1016/j.gecco.2022.e02143"},{"reference":"Foster ML, Dowd SE, Stephenson C, Steiner JM, Suchodolski JS. 2013. Characterization of the fungal microbiome (mycobiome) in fecal samples from dogs. Vet Med Int 2013: 658373.
","pubmedId":"23738233","doi":""},{"reference":"Garcia-Bustos V, Acosta-Hernández B, Cabañero-Navalón MD, Ruiz-Gaitán AC, Pemán J, Rosario Medina I. 2024. Potential Fungal Zoonotic Pathogens in Cetaceans: An Emerging Concern. Microorganisms 12(3): 10.3390/microorganisms12030554.
","pubmedId":"38543604","doi":""},{"reference":"García-De La Peña C, Garduño-Niño E, Vaca-Paniagua F, Díaz-Velásquez C, Barrows CW, Gomez-Gil B, Valenzuela-Núñez, LM. 2019. Comparison of the fecal bacterial microbiota composition between wild and captive bolson tortoises (Gopherus flavomarginatus). Herpetol Conserv Bio 14 :587–600.
","pubmedId":"","doi":""},{"reference":"Giakoumas DS, Moore J, Stamper E, Bernot KM, Mincer TJ. 2024. State-threatened gopher tortoise (Gopherus polyphemus) gut microbiome analysis reveals health insights into southeastern Florida population. BioRxiv.
","pubmedId":"","doi":""},{"reference":"Guinea J. 2014. Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect 20 Suppl 6: 5-10.
","pubmedId":"24506442","doi":""},{"reference":"Hong PY, Wheeler E, Cann IK, Mackie RI. 2011. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. ISME J 5(9): 1461-70.
","pubmedId":"21451584","doi":""},{"reference":"Huffman JN, Haizlett KS, Elhassani DK, Cooney BT, Frazier EM. 2018. A Survey of Gopherus polyphemus Intestinal Parasites in South Florida. J Parasitol Res 2018: 3048795.
","pubmedId":"30687545","doi":""},{"reference":"Jones M, Loope K, Porter V, Walkup D, Ryberg W, Preston J, Johnson J, Hagedorn B, Bilbow R, Moore B, Bowers BC, Lopez RR, Hunter EA. 2025. Aggregated space use by soft-released translocated gopher tortoises (Gopherus polyphemus). Herpetologica 81: 141–151.
","pubmedId":"","doi":""},{"reference":"Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, et al., Zhang XX. 2023. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 11(1): e0242422.
","pubmedId":"36625628","doi":""},{"reference":"McDonald JE, Rooks DJ, McCarthy AJ. 2012. Methods for the isolation of cellulose-degrading microorganisms. Methods Enzymol 510: 349-74.
","pubmedId":"22608736","doi":""},{"reference":"Pinto TN, Costa GLD, Costa MAT, Lima ÉVDS, Carvalho TRC, Santos JDS, et al., Oliveira MME. 2025. Screening of yeasts in the oral microbiota of bats (Chiroptera) in Piauí, Brazil. New Microbes New Infect 67: 101628.
","pubmedId":"40980201","doi":""},{"reference":"Sanchez FA, Dowd SE, Brandt J, McLaughlin RW. 2021. Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus. Arch Microbiol 204(1): 42.
","pubmedId":"34932157","doi":""},{"reference":"Sandri C, Correa F, Spiezio C, Trevisi P, Luise D, Modesto M, et al., Mattarelli P. 2020. Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments. Front Microbiol 11: 569249.
","pubmedId":"33193160","doi":""},{"reference":"Scott CM, Holman DB, Gzyl KE, Ibe A, Taheri AE. 2025. Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine. Microb Ecol 88(1): 104.
","pubmedId":"41037066","doi":""},{"reference":"Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H. 2020. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol 10: 151.
","pubmedId":"32328469","doi":""},{"reference":"Ugochukwu ICI, Mendoza-Roldan JA, Rhimi W, Miglianti M, Odigie AE, Mosca A, et al., Cafarchia C. 2024. Snakes as sentinel of zoonotic yeasts and bio-indicators of environmental quality. Sci Rep 14(1): 22491.
","pubmedId":"39341972","doi":""},{"reference":"Webster J. 1970. Coprophilous fungi. Transactions of the British Mycological Society 54: 161-180.
","pubmedId":"","doi":""},{"reference":"Whitfield SM, Scholl JP, Frazier EM, Hendrickson K, Figueroa A, Gapczynski L, et al., Moore. 2024. Status, Distribution, and Management of Gopher Tortoises in Highly Urbanized Southeastern Florida. Southeastern Naturalist 23: 10.1656/058.023.0311.
","pubmedId":"","doi":"10.1656/058.023.0311"},{"reference":"Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. 2015. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 24(10): 2521-36.
","pubmedId":"25809385","doi":""}],"title":"An analysis of the bacterial and fungal diversity of the fecal material of Gopher Tortoises
","reviews":[{"reviewer":{"displayName":"Kristina Blanke"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"d25b897c-fc9f-494f-8ac1-104045a34bf8","decision":"revise","abstract":"The gopher tortoise (Gopherus polyphemus) is listed in the State of Florida as a threatened species. It is well known that the microbiota of the host is imperative to health promotion and disease mitigation. The diversity of the gut microbiota of the tortoise has not been extensively surveyed. In this study, we examined both the bacterial and fungal diversity in the fecal material of this animal using bacterial tag-encoded flexible-Titanium (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded FLX amplicon pyrosequencing. In the six samples, there were 16 total bacterial phyla identified with Bacillota (54.55 to 86.13%) as the most dominant and two fungal phyla identified with Ascomycota (79.64 to 97.32%) as the most predominant. Interestingly, the pathogenic fungus Candida tropicalis was detected in all samples suggesting the tortoise could be a reservoir of zoonotic fungi.
","acknowledgements":"This research was done as part of a High Honors project under the leadership of Matthew Janisin, Executive Vice-President (EVP). We thank Maxwell Banor, Nicole Dutton and Donald Zakutansky for their enthusiastic support of this research. We thank Tricia LaPointe, executive director, and Valerie Wolfrey, curator, at the Peace River Wildlife Center (PRWC). We also thank Kellie Reitzel for placing us in contact with members of the PRWC.
","authors":[{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["methodology","writing_originalDraft","writing_reviewEditing"],"email":"vankonil1@mail.gtc.edu","firstName":"Lauren M.K.","lastName":"Vankoningsveld","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["conceptualization","fundingAcquisition","writing_originalDraft","writing_reviewEditing"],"email":"mclaughlinr@gtc.edu","firstName":"Richard W.","lastName":"McLaughlin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-4634-7096"},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["investigation","methodology","writing_originalDraft"],"email":"bevisd@gtc.edu","firstName":"Durward L.","lastName":"Bevis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/23c7c1f1b35a42cc575165cc40500866.csv"},"extendedData":[],"funding":"This project was supported by funding provided by Gateway Technical College and by the Gateway Foundation.
","image":{"url":null},"imageCaption":"An analysis of the Predicted Bacterial Phyla (1A), Predicted Bacterial Genera (1B), Bacterial Information (1C), Predicted Fungal Phyla (1D), Predicted Fungal Genera (1E), and Fungal Information (1F). The values listed in sections 1A, 1B, 1D, and 1E represent a relative percentage of zero-radius operational taxonomic units (ZOTUs).
","imageTitle":"
Bacterial and fungal diversity present in the fecal material of two gopher tortoises
","methods":"Animals and sample collection
The two gopher tortoises in this study live at the Peace River Wildlife Center Punta Gorda, Florida. Ruffles is a 61-year-old female, with severe metabolic bone disease (MBD) from many years of incorrect husbandry which has resulted in a disfigured shell. The shell length is 9 inches. Legolas is a female of unknown age with a shell length of 14.5 inches. Three samples from each tortoise were collected over an approximate one-month period of time and placed into separate containers. The date of sampling is found in Table 1. All samples were transported and then stored in a − 40 °C freezer until used.
Microbiota analysis
The bacterial diversity and the fungal diversity within the six-gopher tortoise fecal samples used for our study were determined using bTEFAP® services. These assays were performed by MR DNA (Shallowater, TX). Primers 515F-806 (forward: GAG TTT GAT CNT GGC TCA G;
reverse: GTN TTA CNG CGG CKG CTG) and ITS1-2 (forward: CTT GGT CAT TTA GAG GAA GTA A; reverse: GCT GCG TTC TTC ATC GAT GC) were used to amplify bacterial and fungal DNA, respectively. A more detailed explanation of the methods can be found in the study by Sanchez et al., 2021.
","reagents":"","patternDescription":"Gopher tortoises (Gopherus polyphemus) are mostly found in the Southeastern United States and along the Coastal Plains. Gopher tortoises are listed as a threatened species by the State of Florida (Florida Fish and Wildlife Commission, 2025). These animals often burrow in dry sandy environments (Florida Fish and Wildlife Commission, 2025). However, they are subjected to numerous problems including habitat degradation and forced relocation. This can result in an unnatural mixing of the populations and an increased exposure to harmful parasites and disease (Huffman et al., 2018; Cozad et al., 2020; Folt et al., 2022; Whitfield et al., 2024; Jones et al., 2025).
The diet of many tortoise species generally includes flowers, fruit, legumes, and several varieties of grass. (Abella and Berry, 2016; Figueroa et al., 2024). Though the diet of tortoises is well known, the information regarding the gut microbiome is lacking, which is not uncommon for reptilian herbivores (Sandri et al., 2020). This scarcity of information limits our understanding of the disease process and resilience of the animal.
In this current study amplicon sequencing was performed to obtain an inventory of the bacterial and fungal diversity in the fecal material of two gopher tortoises, Ruffles and Legolas, living at the Peace River Wildlife Center in Punta Gorda, Florida. As a noninvasive technique, fecal samples are often utilized to examine the gut microbiome of animals (Tang et al., 2020). Three samples from each tortoise were collected over a one-month period of time. The average number of sequences and ZOTUs for Ruffles’ bacterial diversity was 29429 and 402, respectively. The average number of sequences and ZOTUs for Legolas’ bacterial diversity was 29442 and 410, respectively. The most abundant bacterial phylum in all samples was Bacillota (formerly firmicutes), followed by Pseudomonadota (formerly Proteobacteria). The most predominant genus found in four of the samples was Clostridium (Table 1).
In terms of fungi, the average number of sequences and ZOTUs for Ruffles was 28107 and 185, respectively. The average number of sequences and ZOTUs for Legolas was 29200 and 183, respectively. The most abundant fungal phylum throughout the samples was Ascomycota. Candida was the most abundant genera in four of the six samples (Table 1).
Amplicon sequencing has been used to assess the fecal microbiome in different tortoise species. In the Seychelles giant tortoises (Aldabrachelys gigantea) living in different environments the most abundant phyla were Bacteroidota (42.00%), Bacillota (32.00%), and Spirochaetota (9.00%) (Sandri et al., 2020). In desert tortoises Bacillota, Bacteroidota, and Actinobacteroidota comprised the majority of the phyla found in the samples (Blair et al., 2025). In captive Bolson tortoises (Gopherus flavomarginatus) the most abundant phylum was Bacillota followed by Fibrobacterota (García-De La Peña et al., 2019). In a previous study examining the bacterial diversity in the fecal material of a south-central Florida population of gopher tortoises, the most predominant phyla were the Bacillota (36.00%) and Bacteroidetes (36.50%) (Yang et al., 2015). In a more recent study examining a population living in Abacoa Greenway in Jupiter, Florida, 20 different phyla were identified with Bacillota (70.44%) as the most predominant (Giakoumas et al., 2024). In our study, the average percentage of Bacillota for Ruffles was 70.35, and for Legalos was 71.60 which is much higher than detected in the study completed by Yang et al., (2015), but very similar to the results found in the study Giakoumas et al., (2024). Our findings were more consistent with those of previous studies conducted on herbivorous reptiles. For example, in the Galapagos tortoise (Chelonoidis nigra), the green iguana (Iguana iguana), and the marine iguana (Amblyrhynchus cristatus) the relative abundance of Bacillota was 81.10%, 74.00% and 75.10%, respectively (Hong et al., 2011).
In our study, in terms of fungal diversity there were only two phyla present, Ascomycota and Basidiomycota (Table 1). In previous gopher tortoise studies, the fungal diversity was not examined. It has been documented that in the fecal material of reptiles these two phyla are seldomly found (Weber, 1970). Ascomycota and Basidiomycota are major decomposers of plant cell walls. Specifically, Ascomycetes are primarily responsible for the digestion of cellulose and hemicellulose, whereas Basidiomycetes are more active in lignin degradation (Manici et al., 2024). These fungi are commonly detected in the gastrointestinal tracts of animals and often dominate the gut mycobiota, particularly in herbivores consuming a plant-rich diet (Zhao et al., 2023; Lv et al., 2023).
The breakdown of dietary cellulose and hemicellulose can also be accomplished by cellulolytic bacteria. Many such bacteria that are found within the phyla Bacillota as well as Bacteroidetes are capable of cellulose digestion (Bhatia et al., 2024). The gopher tortoise is a hindgut fermenter that utilizes microbial fermentation of starch in the hindgut. Unnamed bacterial taxa likely play an important role in the metabolism of the animal and warrant further investigation (Giakoumas et al., 2024). However, this is also likely true of the fungal taxa.
Finally, it is well known animals can be reservoirs for pathogens. In a previous study involving gopher tortoises the potential pathogens Mycoplasmaceae sp., and Helicobacter sp. were detected (Giakoumas et al., 2024). These bacterial species were not detected in this current study. In our study we detected Candida tropicalis with a range of 1.41–75.00% of the sequences for Ruffles and 2.31-92.20% of the sequences for Legolas. This zoonotic fungal species has been detected in the Puff adder (Bitis arietans), the Moroccan cobra (Naja haje legionis) (Ugochukwu et al., 2024), bats (Pinto et al., 2025), cetaceans (Garcia-Bustos et al., 2024), cows (Clarke, 1960), goats, sheep, psittacines, rhea monkeys, horses, sirenians, and shrimp (Cordeiro Rde et al., 2014). This yeast can cause mastitis in cows (Clarke, 1960), blood stream infections in humans (Guinea, 2014) and oropharyngeal candidiasis (Collins et al., 2011). In conclusion, our study reaffirms the role of animals as reservoirs for zoonotic microorganisms. These findings underscore the importance of continued surveillance of microbial communities in animals to better understand pathogen distribution and potential risks to human health.
","references":[{"reference":"Abella SR, Berry KH. 2016. Enhancing and Restoring Habitat for the Desert Tortoise. Journal of Fish and Wildlife Management 7: 255-279.
","pubmedId":"","doi":"10.3996/052015-JFWM-046"},{"reference":"Bhatia T, Bose D, Sharma D, Patel D. 2024. A Review on Cellulose Degrading Microbes and its Applications. Industrial Biotechnology 20: 26-39.
","pubmedId":"","doi":"10.1089/ind.2023.0025"},{"reference":"Blair EM, Margalith NJ, O’Malley MA. 2025. Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota. Microbial Ecology 88: 10.1007/s00248-025-02557-6.
","pubmedId":"","doi":"10.1007/s00248-025-02557-6"},{"reference":"Clarke RTJ. 1960. Rumen Candida species and bovine mastitis. New Zealand Veterinary Journal 8: 79-79.
","pubmedId":"","doi":"10.1080/00480169.1960.33385"},{"reference":"Collins CD, Cookinham S, Smith J. 2011. Management of oropharyngeal candidiasis with localized oral miconazole therapy: efficacy, safety, and patient acceptability. Patient Prefer Adherence 5: 369-74.
","pubmedId":"21845036","doi":"10.2147/PPA.S14047"},{"reference":"Cordeiro Rde A, de Oliveira JS, Castelo-Branco Dde S, Teixeira CE, Marques FJ, Bittencourt PV, et al., Rocha MF. 2015. Candida tropicalis isolates obtained from veterinary sources show resistance to azoles and produce virulence factors. Med Mycol 53(2): 145-52.
","pubmedId":"25550392","doi":""},{"reference":"Cozad RA, Hernandez SM, Norton TM, Tuberville TD, Stacy NI, Stedman NL, Aresco MJ. 2020. Epidemiological Investigation of a Mortality Event in a Translocated Gopher Tortoise (Gopherus polyphemus) Population in Northwest Florida. Front Vet Sci 7: 120.
","pubmedId":"32211432","doi":""},{"reference":"Florida Fish and Wildlife Commission [FFWC] Gopher Tortoise Management Plan. Florida Fish and Wildlife Commission; Tallahassee, FL, USA: 2024. [(accessed on 15 July 2025)]. Available online: https://myfwc.com/media/xd1icqci/gtmgmtplan2024.pdf
","pubmedId":"","doi":""},{"reference":"Figueroa A, Coblentz K, Herrera A, Cuni L, Villate J, Liu H, Araujo MS, Whitfield SM. 2024. Seasonal Frugivory Facilitates Individual Diet Specialization in the Generalist Herbivore Gopher Tortoise. : 10.2139/ssrn.4822385.
","pubmedId":"","doi":"10.2139/ssrn.4822385"},{"reference":"Folt B, Marshall M, Emanuel JA, Dziadzio M, Cooke J, Mena L, et al., McGowan. 2022. Using predictions from multiple anthropogenic threats to estimate future population persistence of an imperiled species. Global Ecology and Conservation 36: e02143.
","pubmedId":"","doi":"10.1016/j.gecco.2022.e02143"},{"reference":"Garcia-Bustos V, Acosta-Hernández B, Cabañero-Navalón MD, Ruiz-Gaitán AC, Pemán J, Rosario Medina I. 2024. Potential Fungal Zoonotic Pathogens in Cetaceans: An Emerging Concern. Microorganisms 12(3): 10.3390/microorganisms12030554.
","pubmedId":"38543604","doi":""},{"reference":"García-De La Peña C, Garduño-Niño E, Vaca-Paniagua F, Díaz-Velásquez C, Barrows CW, Gomez-Gil B, Valenzuela-Núñez, LM. 2019. Comparison of the fecal bacterial microbiota composition between wild and captive bolson tortoises (Gopherus flavomarginatus). Herpetol Conserv Bio 14 :587–600.
","pubmedId":"","doi":""},{"reference":"Giakoumas DS, Moore J, Stamper E, Bernot KM, Mincer TJ. 2024. State-threatened gopher tortoise (Gopherus polyphemus) gut microbiome analysis reveals health insights into southeastern Florida population. BioRxiv.
","pubmedId":"","doi":""},{"reference":"Guinea J. 2014. Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect 20 Suppl 6: 5-10.
","pubmedId":"24506442","doi":""},{"reference":"Hong PY, Wheeler E, Cann IK, Mackie RI. 2011. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. ISME J 5(9): 1461-70.
","pubmedId":"21451584","doi":""},{"reference":"Huffman JN, Haizlett KS, Elhassani DK, Cooney BT, Frazier EM. 2018. A Survey of Gopherus polyphemus Intestinal Parasites in South Florida. J Parasitol Res 2018: 3048795.
","pubmedId":"30687545","doi":""},{"reference":"Jones M, Loope K, Porter V, Walkup D, Ryberg W, Preston J, Johnson J, Hagedorn B, Bilbow R, Moore B, Bowers BC, Lopez RR, Hunter EA. 2025. Aggregated space use by soft-released translocated gopher tortoises (Gopherus polyphemus). Herpetologica 81: 141–151.
","pubmedId":"","doi":""},{"reference":"Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, et al., Zhang XX. 2023. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 11(1): e0242422.
","pubmedId":"36625628","doi":""},{"reference":"Pinto TN, Costa GLD, Costa MAT, Lima ÉVDS, Carvalho TRC, Santos JDS, et al., Oliveira MME. 2025. Screening of yeasts in the oral microbiota of bats (Chiroptera) in Piauí, Brazil. New Microbes New Infect 67: 101628.
","pubmedId":"40980201","doi":""},{"reference":"Sanchez FA, Dowd SE, Brandt J, McLaughlin RW. 2021. Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus. Arch Microbiol 204(1): 42.
","pubmedId":"34932157","doi":""},{"reference":"Sandri C, Correa F, Spiezio C, Trevisi P, Luise D, Modesto M, et al., Mattarelli P. 2020. Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments. Front Microbiol 11: 569249.
","pubmedId":"33193160","doi":""},{"reference":"Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H. 2020. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol 10: 151.
","pubmedId":"32328469","doi":""},{"reference":"Ugochukwu ICI, Mendoza-Roldan JA, Rhimi W, Miglianti M, Odigie AE, Mosca A, et al., Cafarchia C. 2024. Snakes as sentinel of zoonotic yeasts and bio-indicators of environmental quality. Sci Rep 14(1): 22491.
","pubmedId":"39341972","doi":""},{"reference":"Webster J. 1970. Coprophilous fungi. Transactions of the British Mycological Society 54: 161-180.
","pubmedId":"","doi":""},{"reference":"Whitfield SM, Scholl JP, Frazier EM, Hendrickson K, Figueroa A, Gapczynski L, et al., Moore. 2024. Status, Distribution, and Management of Gopher Tortoises in Highly Urbanized Southeastern Florida. Southeastern Naturalist 23: 10.1656/058.023.0311.
","pubmedId":"","doi":"10.1656/058.023.0311"},{"reference":"Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. 2015. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 24(10): 2521-36.
","pubmedId":"25809385","doi":""},{"reference":"Zhao Y, Ren X, Wu H, Hu H, Cheng C, Du M, et al., Dugarjaviin M. 2023. Diversity and functional prediction of fungal communities in different segments of mongolian horse gastrointestinal tracts. BMC Microbiol 23(1): 253.
","pubmedId":"37689675","doi":""}],"title":"An analysis of the bacterial and fungal diversity of the fecal material of gopher tortoises
","reviews":[{"reviewer":{"displayName":"Kristina Blanke"},"openAcknowledgement":null,"status":{"submitted":false}}],"curatorReviews":[]},{"id":"7c453640-3d55-4fb4-ad20-2cee037afc54","decision":"accept","abstract":"The gopher tortoise (Gopherus polyphemus) is listed in the State of Florida as a threatened species. It is well known that the microbiota of the host is imperative to health promotion and disease mitigation. The diversity of the gut microbiota of the tortoise has not been extensively surveyed. In this study, we examined both the bacterial and fungal diversity in the fecal material of this animal using bacterial tag-encoded flexible-Titanium (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded FLX amplicon pyrosequencing. In the six samples, there were 16 total bacterial phyla identified with Bacillota (54.55 to 86.13%) as the most dominant and two fungal phyla identified with Ascomycota (79.64 to 97.32%) as the most predominant. Interestingly, the pathogenic fungus Candida tropicalis was detected in all samples suggesting the tortoise could be a reservoir of zoonotic fungi.
","acknowledgements":"This research was done as part of a High Honors project under the leadership of Matthew Janisin, Executive Vice-President (EVP). We thank Maxwell Banor, Nicole Dutton and Donald Zakutansky for their enthusiastic support of this research. We thank Tricia LaPointe, executive director, and Valerie Wolfrey, curator, at the Peace River Wildlife Center (PRWC). We also thank Kellie Reitzel for placing us in contact with members of the PRWC.
","authors":[{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["methodology","writing_originalDraft","writing_reviewEditing"],"email":"vankonil1@mail.gtc.edu","firstName":"Lauren M.K.","lastName":"Vankoningsveld","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["conceptualization","fundingAcquisition","writing_originalDraft","writing_reviewEditing"],"email":"mclaughlinr@gtc.edu","firstName":"Richard W.","lastName":"McLaughlin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-4634-7096"},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["investigation","methodology","writing_originalDraft"],"email":"bevisd@gtc.edu","firstName":"Durward L.","lastName":"Bevis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/f9ef6d9e5d313a8ed83849c831e5b0e6.csv"},"extendedData":[],"funding":"This project was supported by funding provided by Gateway Technical College and by the Gateway Foundation.
","image":{"url":null},"imageCaption":"An analysis of the Predicted Bacterial Phyla (1A), Predicted Bacterial Genera (1B), Bacterial Information (1C), Predicted Fungal Phyla (1D), Predicted Fungal Genera (1E), and Fungal Information (1F). The values listed in sections 1A, 1B, 1D, and 1E represent a relative percentage of zero-radius operational taxonomic units (ZOTUs).
","imageTitle":"
Bacterial and fungal diversity present in the fecal material of two gopher tortoises
","methods":"Animals and sample collection
The two gopher tortoises in this study live at the Peace River Wildlife Center Punta Gorda, Florida. Ruffles is a 61-year-old female, with severe metabolic bone disease (MBD) from many years of incorrect husbandry which has resulted in a disfigured shell. The shell length is 9 inches. Legolas is a female of unknown age with a shell length of 14.5 inches. Three samples from each tortoise were collected over an approximate one-month period of time and placed into separate containers. The date of sampling is found in Table 1. All samples were transported and then stored in a − 40 °C freezer until used.
Microbiota analysis
The bacterial diversity and the fungal diversity within the six-gopher tortoise fecal samples used for our study were determined using bTEFAP® services. These assays were performed by MR DNA (Shallowater, TX). Primers 515F-806 (forward: GAG TTT GAT CNT GGC TCA G;
reverse: GTN TTA CNG CGG CKG CTG) and ITS1-2 (forward: CTT GGT CAT TTA GAG GAA GTA A; reverse: GCT GCG TTC TTC ATC GAT GC) were used to amplify bacterial and fungal DNA, respectively. A more detailed explanation of the methods can be found in the study by Sanchez et al., 2021.
","reagents":"","patternDescription":"Gopher tortoises (Gopherus polyphemus) are mostly found in the Southeastern United States and along the Coastal Plains. Gopher tortoises are listed as a threatened species by the State of Florida (Florida Fish and Wildlife Commission, 2025). These animals often burrow in dry sandy environments (Florida Fish and Wildlife Commission, 2025). However, they are subjected to numerous problems including habitat degradation and forced relocation. This can result in an unnatural mixing of the populations and an increased exposure to harmful parasites and disease (Huffman et al., 2018; Cozad et al., 2020; Folt et al., 2022; Whitfield et al., 2024; Jones et al., 2025).
The diet of many tortoise species generally includes flowers, fruit, legumes, and several varieties of grass. (Abella and Berry, 2016; Figueroa et al., 2024). Though the diet of tortoises is well known, the information regarding the gut microbiome is lacking, which is not uncommon for reptilian herbivores (Sandri et al., 2020). This scarcity of information limits our understanding of the disease process and resilience of the animal.
In this current study amplicon sequencing was performed to obtain an inventory of the bacterial and fungal diversity in the fecal material of two gopher tortoises, Ruffles and Legolas, living at the Peace River Wildlife Center in Punta Gorda, Florida. As a noninvasive technique, fecal samples are often utilized to examine the gut microbiome of animals (Tang et al., 2020). Three samples from each tortoise were collected over a one-month period of time. The average number of sequences and ZOTUs for Ruffles’ bacterial diversity was 29429 and 402, respectively. The average number of sequences and ZOTUs for Legolas’ bacterial diversity was 29442 and 410, respectively. The most abundant bacterial phylum in all samples was Bacillota (formerly firmicutes), followed by Pseudomonadota (formerly Proteobacteria). The most predominant genus found in four of the samples was Clostridium (Table 1).
In terms of fungi, the average number of sequences and ZOTUs for Ruffles was 28107 and 185, respectively. The average number of sequences and ZOTUs for Legolas was 29200 and 183, respectively. The most abundant fungal phylum throughout the samples was Ascomycota. Candida was the most abundant genera in four of the six samples (Table 1).
Amplicon sequencing has been used to assess the fecal microbiome in different tortoise species. In the Seychelles giant tortoises (Aldabrachelys gigantea) living in different environments the most abundant phyla were Bacteroidota (42.00%), Bacillota (32.00%), and Spirochaetota (9.00%) (Sandri et al., 2020). In desert tortoises Bacillota, Bacteroidota, and Actinobacteroidota comprised the majority of the phyla found in the samples (Blair et al., 2025). In captive Bolson tortoises (Gopherus flavomarginatus) the most abundant phylum was Bacillota followed by Fibrobacterota (García-De La Peña et al., 2019). In a previous study examining the bacterial diversity in the fecal material of a south-central Florida population of gopher tortoises, the most predominant phyla were the Bacillota (36.00%) and Bacteroidetes (36.50%) (Yang et al., 2015). In a more recent study examining a population living in Abacoa Greenway in Jupiter, Florida, 20 different phyla were identified with Bacillota (70.44%) as the most predominant (Giakoumas et al., 2024). In our study, the average percentage of Bacillota for Ruffles was 70.35, and for Legalos was 71.60 which is much higher than detected in the study completed by Yang et al., (2015), but very similar to the results found in the study Giakoumas et al., (2024). Our findings were more consistent with those of previous studies conducted on herbivorous reptiles. For example, in the Galapagos tortoise (Chelonoidis nigra), the green iguana (Iguana iguana), and the marine iguana (Amblyrhynchus cristatus) the relative abundance of Bacillota was 81.10%, 74.00% and 75.10%, respectively (Hong et al., 2011).
In our study, in terms of fungal diversity there were only two phyla present, Ascomycota and Basidiomycota (Table 1). In previous gopher tortoise studies, the fungal diversity was not examined. It has been documented that in the fecal material of reptiles these two phyla are seldomly found (Weber, 1970). Ascomycota and Basidiomycota are major decomposers of plant cell walls. Specifically, Ascomycetes are primarily responsible for the digestion of cellulose and hemicellulose, whereas Basidiomycetes are more active in lignin degradation (Manici et al., 2024). These fungi are commonly detected in the gastrointestinal tracts of animals and often dominate the gut mycobiota, particularly in herbivores consuming a plant-rich diet (Zhao et al., 2023; Lv et al., 2023).
The breakdown of dietary cellulose and hemicellulose can also be accomplished by cellulolytic bacteria. Many such bacteria that are found within the phyla Bacillota as well as Bacteroidetes are capable of cellulose digestion (Bhatia et al., 2024). The gopher tortoise is a hindgut fermenter that utilizes microbial fermentation of starch in the hindgut. Unnamed bacterial taxa likely play an important role in the metabolism of the animal and warrant further investigation (Giakoumas et al., 2024). However, this is also likely true of the fungal taxa.
Finally, it is well known animals can be reservoirs for pathogens. In a previous study involving gopher tortoises the potential pathogens Mycoplasmaceae sp., and Helicobacter sp. were detected (Giakoumas et al., 2024). These bacterial species were not detected in this current study. In our study we detected Candida tropicalis with a range of 1.41–75.00% of the sequences for Ruffles and 2.31-92.20% of the sequences for Legolas. This zoonotic fungal species has been detected in the Puff adder (Bitis arietans), the Moroccan cobra (Naja haje legionis) (Ugochukwu et al., 2024), bats (Pinto et al., 2025), cetaceans (Garcia-Bustos et al., 2024), cows (Clarke, 1960), goats, sheep, psittacines, rhea monkeys, horses, sirenians, and shrimp (Cordeiro Rde et al., 2014). This yeast can cause mastitis in cows (Clarke, 1960), blood stream infections in humans (Guinea, 2014) and oropharyngeal candidiasis (Collins et al., 2011). In conclusion, our study reaffirms the role of animals as reservoirs for zoonotic microorganisms. These findings underscore the importance of continued surveillance of microbial communities in animals to better understand pathogen distribution and potential risks to human health.
","references":[{"reference":"Abella SR, Berry KH. 2016. Enhancing and Restoring Habitat for the Desert Tortoise. Journal of Fish and Wildlife Management 7: 255-279.
","pubmedId":"","doi":"10.3996/052015-JFWM-046"},{"reference":"Bhatia T, Bose D, Sharma D, Patel D. 2024. A Review on Cellulose Degrading Microbes and its Applications. Industrial Biotechnology 20: 26-39.
","pubmedId":"","doi":"10.1089/ind.2023.0025"},{"reference":"Blair EM, Margalith NJ, O’Malley MA. 2025. Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota. Microbial Ecology 88: 10.1007/s00248-025-02557-6.
","pubmedId":"","doi":"10.1007/s00248-025-02557-6"},{"reference":"Clarke RTJ. 1960. Rumen Candida species and bovine mastitis. New Zealand Veterinary Journal 8: 79-79.
","pubmedId":"","doi":"10.1080/00480169.1960.33385"},{"reference":"Collins CD, Cookinham S, Smith J. 2011. Management of oropharyngeal candidiasis with localized oral miconazole therapy: efficacy, safety, and patient acceptability. Patient Prefer Adherence 5: 369-74.
","pubmedId":"21845036","doi":"10.2147/PPA.S14047"},{"reference":"Cordeiro Rde A, de Oliveira JS, Castelo-Branco Dde S, Teixeira CE, Marques FJ, Bittencourt PV, et al., Rocha MF. 2015. Candida tropicalis isolates obtained from veterinary sources show resistance to azoles and produce virulence factors. Med Mycol 53(2): 145-52.
","pubmedId":"25550392","doi":""},{"reference":"Cozad RA, Hernandez SM, Norton TM, Tuberville TD, Stacy NI, Stedman NL, Aresco MJ. 2020. Epidemiological Investigation of a Mortality Event in a Translocated Gopher Tortoise (Gopherus polyphemus) Population in Northwest Florida. Front Vet Sci 7: 120.
","pubmedId":"32211432","doi":""},{"reference":"Florida Fish and Wildlife Commission [FFWC] Gopher Tortoise Management Plan. Florida Fish and Wildlife Commission; Tallahassee, FL, USA: 2024. [(accessed on 15 July 2025)]. Available online: https://myfwc.com/media/xd1icqci/gtmgmtplan2024.pdf
","pubmedId":"","doi":""},{"reference":"Figueroa A, Coblentz K, Herrera A, Cuni L, Villate J, Liu H, Araujo MS, Whitfield SM. 2024. Seasonal Frugivory Facilitates Individual Diet Specialization in the Generalist Herbivore Gopher Tortoise. : 10.2139/ssrn.4822385.
","pubmedId":"","doi":"10.2139/ssrn.4822385"},{"reference":"Folt B, Marshall M, Emanuel JA, Dziadzio M, Cooke J, Mena L, et al., McGowan. 2022. Using predictions from multiple anthropogenic threats to estimate future population persistence of an imperiled species. Global Ecology and Conservation 36: e02143.
","pubmedId":"","doi":"10.1016/j.gecco.2022.e02143"},{"reference":"Garcia-Bustos V, Acosta-Hernández B, Cabañero-Navalón MD, Ruiz-Gaitán AC, Pemán J, Rosario Medina I. 2024. Potential Fungal Zoonotic Pathogens in Cetaceans: An Emerging Concern. Microorganisms 12(3): 10.3390/microorganisms12030554.
","pubmedId":"38543604","doi":""},{"reference":"García-De La Peña C, Garduño-Niño E, Vaca-Paniagua F, Díaz-Velásquez C, Barrows CW, Gomez-Gil B, Valenzuela-Núñez, LM. 2019. Comparison of the fecal bacterial microbiota composition between wild and captive bolson tortoises (Gopherus flavomarginatus). Herpetol Conserv Bio 14 :587–600.
","pubmedId":"","doi":""},{"reference":"Giakoumas DS, Moore J, Stamper E, Bernot KM, Mincer TJ. 2024. State-threatened gopher tortoise (Gopherus polyphemus) gut microbiome analysis reveals health insights into southeastern Florida population. BioRxiv.
","pubmedId":"","doi":""},{"reference":"Guinea J. 2014. Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect 20 Suppl 6: 5-10.
","pubmedId":"24506442","doi":""},{"reference":"Hong PY, Wheeler E, Cann IK, Mackie RI. 2011. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. ISME J 5(9): 1461-70.
","pubmedId":"21451584","doi":""},{"reference":"Huffman JN, Haizlett KS, Elhassani DK, Cooney BT, Frazier EM. 2018. A Survey of Gopherus polyphemus Intestinal Parasites in South Florida. J Parasitol Res 2018: 3048795.
","pubmedId":"30687545","doi":""},{"reference":"Jones M, Loope K, Porter V, Walkup D, Ryberg W, Preston J, Johnson J, Hagedorn B, Bilbow R, Moore B, Bowers BC, Lopez RR, Hunter EA. 2025. Aggregated space use by soft-released translocated gopher tortoises (Gopherus polyphemus). Herpetologica 81: 141–151.
","pubmedId":"","doi":""},{"reference":"Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, et al., Zhang XX. 2023. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 11(1): e0242422.
","pubmedId":"36625628","doi":""},{"reference":"Pinto TN, Costa GLD, Costa MAT, Lima ÉVDS, Carvalho TRC, Santos JDS, et al., Oliveira MME. 2025. Screening of yeasts in the oral microbiota of bats (Chiroptera) in Piauí, Brazil. New Microbes New Infect 67: 101628.
","pubmedId":"40980201","doi":""},{"reference":"Sanchez FA, Dowd SE, Brandt J, McLaughlin RW. 2021. Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus. Arch Microbiol 204(1): 42.
","pubmedId":"34932157","doi":""},{"reference":"Sandri C, Correa F, Spiezio C, Trevisi P, Luise D, Modesto M, et al., Mattarelli P. 2020. Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments. Front Microbiol 11: 569249.
","pubmedId":"33193160","doi":""},{"reference":"Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H. 2020. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol 10: 151.
","pubmedId":"32328469","doi":""},{"reference":"Ugochukwu ICI, Mendoza-Roldan JA, Rhimi W, Miglianti M, Odigie AE, Mosca A, et al., Cafarchia C. 2024. Snakes as sentinel of zoonotic yeasts and bio-indicators of environmental quality. Sci Rep 14(1): 22491.
","pubmedId":"39341972","doi":""},{"reference":"Webster J. 1970. Coprophilous fungi. Transactions of the British Mycological Society 54: 161-180.
","pubmedId":"","doi":""},{"reference":"Whitfield SM, Scholl JP, Frazier EM, Hendrickson K, Figueroa A, Gapczynski L, et al., Moore. 2024. Status, Distribution, and Management of Gopher Tortoises in Highly Urbanized Southeastern Florida. Southeastern Naturalist 23: 10.1656/058.023.0311.
","pubmedId":"","doi":"10.1656/058.023.0311"},{"reference":"Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. 2015. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 24(10): 2521-36.
","pubmedId":"25809385","doi":""},{"reference":"Zhao Y, Ren X, Wu H, Hu H, Cheng C, Du M, et al., Dugarjaviin M. 2023. Diversity and functional prediction of fungal communities in different segments of mongolian horse gastrointestinal tracts. BMC Microbiol 23(1): 253.
","pubmedId":"37689675","doi":""}],"title":"An analysis of the bacterial and fungal diversity of the fecal material of gopher tortoises
","reviews":[],"curatorReviews":[]},{"id":"d0b615f4-1b7f-4ea8-aaca-4993e6be18eb","decision":"accept","abstract":"The gopher tortoise (Gopherus polyphemus) is listed in the State of Florida as a threatened species. It is well known that the microbiota of the host is imperative to health promotion and disease mitigation. The diversity of the gut microbiota of the tortoise has not been extensively surveyed. In this study, we examined both the bacterial and fungal diversity in the fecal material of this animal using bacterial tag-encoded flexible-Titanium (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded FLX amplicon pyrosequencing. In the six samples, there were 16 total bacterial phyla identified with Bacillota (54.55 to 86.13%) as the most dominant and two fungal phyla identified with Ascomycota (79.64 to 97.32%) as the most predominant. Interestingly, the pathogenic fungus Candida tropicalis was detected in all samples suggesting the tortoise could be a reservoir of zoonotic fungi.
","acknowledgements":"This research was done as part of a High Honors project under the leadership of Matthew Janisin, Executive Vice-President (EVP). We thank Maxwell Banor, Nicole Dutton and Donald Zakutansky for their enthusiastic support of this research. We thank Tricia LaPointe, executive director, and Valerie Wolfrey, curator, at the Peace River Wildlife Center (PRWC). We also thank Kellie Reitzel for placing us in contact with members of the PRWC.
","authors":[{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["methodology","writing_originalDraft","writing_reviewEditing"],"email":"vankonil1@mail.gtc.edu","firstName":"Lauren M.K.","lastName":"Vankoningsveld","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["conceptualization","fundingAcquisition","writing_originalDraft","writing_reviewEditing"],"email":"mclaughlinr@gtc.edu","firstName":"Richard W.","lastName":"McLaughlin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-4634-7096"},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["investigation","methodology","writing_originalDraft"],"email":"bevisd@gtc.edu","firstName":"Durward L.","lastName":"Bevis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/f9ef6d9e5d313a8ed83849c831e5b0e6.csv"},"extendedData":[],"funding":"This project was supported by funding provided by Gateway Technical College and by the Gateway Foundation.
","image":{"url":null},"imageCaption":"An analysis of the Predicted Bacterial Phyla (1A), Predicted Bacterial Genera (1B), Bacterial Information (1C), Predicted Fungal Phyla (1D), Predicted Fungal Genera (1E), and Fungal Information (1F). The values listed in sections 1A, 1B, 1D, and 1E represent a relative percentage of zero-radius operational taxonomic units (ZOTUs).
","imageTitle":"
Bacterial and fungal diversity present in the fecal material of two gopher tortoises
","methods":"Animals and sample collection
The two gopher tortoises in this study live at the Peace River Wildlife Center Punta Gorda, Florida. Ruffles is a 61-year-old female, with severe metabolic bone disease (MBD) from many years of incorrect husbandry which has resulted in a disfigured shell. The shell length is 9 inches. Legolas is a female of unknown age with a shell length of 14.5 inches. Three samples from each tortoise were collected over an approximate one-month period of time and placed into separate containers. The date of sampling is found in Table 1. All samples were transported and then stored in a − 40 °C freezer until used.
Microbiota analysis
The bacterial diversity and the fungal diversity within the six-gopher tortoise fecal samples used for our study were determined using bTEFAP® services. These assays were performed by MR DNA (Shallowater, TX). Primers 515F-806 (forward: GAG TTT GAT CNT GGC TCA G;
reverse: GTN TTA CNG CGG CKG CTG) and ITS1-2 (forward: CTT GGT CAT TTA GAG GAA GTA A; reverse: GCT GCG TTC TTC ATC GAT GC) were used to amplify bacterial and fungal DNA, respectively. A more detailed explanation of the methods can be found in the study by Sanchez et al., 2021.
","reagents":"","patternDescription":"Gopher tortoises (Gopherus polyphemus) are mostly found in the Southeastern United States and along the Coastal Plains. Gopher tortoises are listed as a threatened species by the State of Florida (Florida Fish and Wildlife Commission, 2025). These animals often burrow in dry sandy environments (Florida Fish and Wildlife Commission, 2025). However, they are subjected to numerous problems including habitat degradation and forced relocation. This can result in an unnatural mixing of the populations and an increased exposure to harmful parasites and disease (Huffman et al., 2018; Cozad et al., 2020; Folt et al., 2022; Whitfield et al., 2024; Jones et al., 2025).
The diet of many tortoise species generally includes flowers, fruit, legumes, and several varieties of grass. (Abella and Berry, 2016; Figueroa et al., 2024). Though the diet of tortoises is well known, the information regarding the gut microbiome is lacking, which is not uncommon for reptilian herbivores (Sandri et al., 2020). This scarcity of information limits our understanding of the disease process and resilience of the animal.
In this current study amplicon sequencing was performed to obtain an inventory of the bacterial and fungal diversity in the fecal material of two gopher tortoises, Ruffles and Legolas, living at the Peace River Wildlife Center in Punta Gorda, Florida. As a noninvasive technique, fecal samples are often utilized to examine the gut microbiome of animals (Tang et al., 2020). Three samples from each tortoise were collected over a one-month period of time. The average number of sequences and ZOTUs for Ruffles’ bacterial diversity was 29429 and 402, respectively. The average number of sequences and ZOTUs for Legolas’ bacterial diversity was 29442 and 410, respectively. The most abundant bacterial phylum in all samples was Bacillota (formerly Firmicutes), followed by Pseudomonadota (formerly Proteobacteria). The most predominant genus found in four of the samples was Clostridium (Table 1).
In terms of fungi, the average number of sequences and ZOTUs for Ruffles was 28107 and 185, respectively. The average number of sequences and ZOTUs for Legolas was 29200 and 183, respectively. The most abundant fungal phylum throughout the samples was Ascomycota. Candida was the most abundant genera in four of the six samples (Table 1).
Amplicon sequencing has been used to assess the fecal microbiome in different tortoise species. In the Seychelles giant tortoises (Aldabrachelys gigantea) living in different environments the most abundant phyla were Bacteroidota (42.00%), Bacillota (32.00%), and Spirochaetota (9.00%) (Sandri et al., 2020). In desert tortoises Bacillota, Bacteroidota, and Actinobacteroidota comprised the majority of the phyla found in the samples (Blair et al., 2025). In captive Bolson tortoises (Gopherus flavomarginatus) the most abundant phylum was Bacillota followed by Fibrobacterota (García-De La Peña et al., 2019). In a previous study examining the bacterial diversity in the fecal material of a south-central Florida population of gopher tortoises, the most predominant phyla were the Bacillota (36.00%) and Bacteroidetes (36.50%) (Yang et al., 2015). In a more recent study examining a population living in Abacoa Greenway in Jupiter, Florida, 20 different phyla were identified with Bacillota (70.44%) as the most predominant (Giakoumas et al., 2024). In our study, the average percentage of Bacillota for Ruffles was 70.35, and for Legalos was 71.60 which is much higher than detected in the study completed by Yang et al., (2015), but very similar to the results found in the study Giakoumas et al., (2024). Our findings were more consistent with those of previous studies conducted on herbivorous reptiles. For example, in the Galapagos tortoise (Chelonoidis nigra), the green iguana (Iguana iguana), and the marine iguana (Amblyrhynchus cristatus) the relative abundance of Bacillota was 81.10%, 74.00% and 75.10%, respectively (Hong et al., 2011).
In our study, in terms of fungal diversity there were only two phyla present, Ascomycota and Basidiomycota (Table 1). In previous gopher tortoise studies, the fungal diversity was not examined. It has been documented that in the fecal material of reptiles these two phyla are seldomly found (Weber, 1970). Ascomycota and Basidiomycota are major decomposers of plant cell walls. Specifically, Ascomycetes are primarily responsible for the digestion of cellulose and hemicellulose, whereas Basidiomycetes are more active in lignin degradation (Manici et al., 2024). These fungi are commonly detected in the gastrointestinal tracts of animals and often dominate the gut mycobiota, particularly in herbivores consuming a plant-rich diet (Zhao et al., 2023; Lv et al., 2023).
The breakdown of dietary cellulose and hemicellulose can also be accomplished by cellulolytic bacteria. Many such bacteria that are found within the phyla Bacillota as well as Bacteroidetes are capable of cellulose digestion (Bhatia et al., 2024). The gopher tortoise is a hindgut fermenter that utilizes microbial fermentation of starch in the hindgut. Unnamed bacterial taxa likely play an important role in the metabolism of the animal and warrant further investigation (Giakoumas et al., 2024). However, this is also likely true of the fungal taxa.
Finally, it is well known animals can be reservoirs for pathogens. In a previous study involving gopher tortoises the potential pathogens Mycoplasmaceae sp., and Helicobacter sp. were detected (Giakoumas et al., 2024). These bacterial species were not detected in this current study. In our study we detected Candida tropicalis with a range of 1.41–75.00% of the sequences for Ruffles and 2.31-92.20% of the sequences for Legolas. This zoonotic fungal species has been detected in the Puff adder (Bitis arietans), the Moroccan cobra (Naja haje legionis) (Ugochukwu et al., 2024), bats (Pinto et al., 2025), cetaceans (Garcia-Bustos et al., 2024), cows (Clarke, 1960), goats, sheep, psittacines, rhea monkeys, horses, sirenians, and shrimp (Cordeiro Rde et al., 2014). This yeast can cause mastitis in cows (Clarke, 1960), blood stream infections in humans (Guinea, 2014) and oropharyngeal candidiasis (Collins et al., 2011). In conclusion, our study reaffirms the role of animals as reservoirs for zoonotic microorganisms. These findings underscore the importance of continued surveillance of microbial communities in animals to better understand pathogen distribution and potential risks to human health.
","references":[{"reference":"Abella SR, Berry KH. 2016. Enhancing and Restoring Habitat for the Desert Tortoise. Journal of Fish and Wildlife Management 7: 255-279.
","pubmedId":"","doi":"10.3996/052015-JFWM-046"},{"reference":"Bhatia T, Bose D, Sharma D, Patel D. 2024. A Review on Cellulose Degrading Microbes and its Applications. Industrial Biotechnology 20: 26-39.
","pubmedId":"","doi":"10.1089/ind.2023.0025"},{"reference":"Blair EM, Margalith NJ, O’Malley MA. 2025. Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota. Microbial Ecology 88: 10.1007/s00248-025-02557-6.
","pubmedId":"","doi":"10.1007/s00248-025-02557-6"},{"reference":"Clarke RTJ. 1960. Rumen Candida species and bovine mastitis. New Zealand Veterinary Journal 8: 79-79.
","pubmedId":"","doi":"10.1080/00480169.1960.33385"},{"reference":"Collins CD, Cookinham S, Smith J. 2011. Management of oropharyngeal candidiasis with localized oral miconazole therapy: efficacy, safety, and patient acceptability. Patient Prefer Adherence 5: 369-74.
","pubmedId":"21845036","doi":"10.2147/PPA.S14047"},{"reference":"Cordeiro Rde A, de Oliveira JS, Castelo-Branco Dde S, Teixeira CE, Marques FJ, Bittencourt PV, et al., Rocha MF. 2015. Candida tropicalis isolates obtained from veterinary sources show resistance to azoles and produce virulence factors. Med Mycol 53(2): 145-52.
","pubmedId":"25550392","doi":""},{"reference":"Cozad RA, Hernandez SM, Norton TM, Tuberville TD, Stacy NI, Stedman NL, Aresco MJ. 2020. Epidemiological Investigation of a Mortality Event in a Translocated Gopher Tortoise (Gopherus polyphemus) Population in Northwest Florida. Front Vet Sci 7: 120.
","pubmedId":"32211432","doi":""},{"reference":"Florida Fish and Wildlife Commission [FFWC] Gopher Tortoise Management Plan. Florida Fish and Wildlife Commission; Tallahassee, FL, USA: 2024. [(accessed on 15 July 2025)]. Available online: https://myfwc.com/media/xd1icqci/gtmgmtplan2024.pdf
","pubmedId":"","doi":""},{"reference":"Figueroa A, Coblentz K, Herrera A, Cuni L, Villate J, Liu H, Araujo MS, Whitfield SM. 2024. Seasonal Frugivory Facilitates Individual Diet Specialization in the Generalist Herbivore Gopher Tortoise. : 10.2139/ssrn.4822385.
","pubmedId":"","doi":"10.2139/ssrn.4822385"},{"reference":"Folt B, Marshall M, Emanuel JA, Dziadzio M, Cooke J, Mena L, et al., McGowan. 2022. Using predictions from multiple anthropogenic threats to estimate future population persistence of an imperiled species. Global Ecology and Conservation 36: e02143.
","pubmedId":"","doi":"10.1016/j.gecco.2022.e02143"},{"reference":"Garcia-Bustos V, Acosta-Hernández B, Cabañero-Navalón MD, Ruiz-Gaitán AC, Pemán J, Rosario Medina I. 2024. Potential Fungal Zoonotic Pathogens in Cetaceans: An Emerging Concern. Microorganisms 12(3): 10.3390/microorganisms12030554.
","pubmedId":"38543604","doi":""},{"reference":"García-De La Peña C, Garduño-Niño E, Vaca-Paniagua F, Díaz-Velásquez C, Barrows CW, Gomez-Gil B, Valenzuela-Núñez, LM. 2019. Comparison of the fecal bacterial microbiota composition between wild and captive bolson tortoises (Gopherus flavomarginatus). Herpetol Conserv Bio 14 :587–600.
","pubmedId":"","doi":""},{"reference":"Giakoumas DS, Moore J, Stamper E, Bernot KM, Mincer TJ. 2024. State-threatened gopher tortoise (Gopherus polyphemus) gut microbiome analysis reveals health insights into southeastern Florida population. BioRxiv.
","pubmedId":"","doi":""},{"reference":"Guinea J. 2014. Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect 20 Suppl 6: 5-10.
","pubmedId":"24506442","doi":""},{"reference":"Hong PY, Wheeler E, Cann IK, Mackie RI. 2011. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. ISME J 5(9): 1461-70.
","pubmedId":"21451584","doi":""},{"reference":"Huffman JN, Haizlett KS, Elhassani DK, Cooney BT, Frazier EM. 2018. A Survey of Gopherus polyphemus Intestinal Parasites in South Florida. J Parasitol Res 2018: 3048795.
","pubmedId":"30687545","doi":""},{"reference":"Jones M, Loope K, Porter V, Walkup D, Ryberg W, Preston J, Johnson J, Hagedorn B, Bilbow R, Moore B, Bowers BC, Lopez RR, Hunter EA. 2025. Aggregated space use by soft-released translocated gopher tortoises (Gopherus polyphemus). Herpetologica 81: 141–151.
","pubmedId":"","doi":""},{"reference":"Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, et al., Zhang XX. 2023. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 11(1): e0242422.
","pubmedId":"36625628","doi":""},{"reference":"Pinto TN, Costa GLD, Costa MAT, Lima ÉVDS, Carvalho TRC, Santos JDS, et al., Oliveira MME. 2025. Screening of yeasts in the oral microbiota of bats (Chiroptera) in Piauí, Brazil. New Microbes New Infect 67: 101628.
","pubmedId":"40980201","doi":""},{"reference":"Sanchez FA, Dowd SE, Brandt J, McLaughlin RW. 2021. Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus. Arch Microbiol 204(1): 42.
","pubmedId":"34932157","doi":""},{"reference":"Sandri C, Correa F, Spiezio C, Trevisi P, Luise D, Modesto M, et al., Mattarelli P. 2020. Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments. Front Microbiol 11: 569249.
","pubmedId":"33193160","doi":""},{"reference":"Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H. 2020. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol 10: 151.
","pubmedId":"32328469","doi":""},{"reference":"Ugochukwu ICI, Mendoza-Roldan JA, Rhimi W, Miglianti M, Odigie AE, Mosca A, et al., Cafarchia C. 2024. Snakes as sentinel of zoonotic yeasts and bio-indicators of environmental quality. Sci Rep 14(1): 22491.
","pubmedId":"39341972","doi":""},{"reference":"Webster J. 1970. Coprophilous fungi. Transactions of the British Mycological Society 54: 161-180.
","pubmedId":"","doi":""},{"reference":"Whitfield SM, Scholl JP, Frazier EM, Hendrickson K, Figueroa A, Gapczynski L, et al., Moore. 2024. Status, Distribution, and Management of Gopher Tortoises in Highly Urbanized Southeastern Florida. Southeastern Naturalist 23: 10.1656/058.023.0311.
","pubmedId":"","doi":"10.1656/058.023.0311"},{"reference":"Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. 2015. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 24(10): 2521-36.
","pubmedId":"25809385","doi":""},{"reference":"Zhao Y, Ren X, Wu H, Hu H, Cheng C, Du M, et al., Dugarjaviin M. 2023. Diversity and functional prediction of fungal communities in different segments of mongolian horse gastrointestinal tracts. BMC Microbiol 23(1): 253.
","pubmedId":"37689675","doi":""}],"title":"An analysis of the bacterial and fungal diversity of the fecal material of gopher tortoises
","reviews":[],"curatorReviews":[]},{"id":"9643029c-b6ff-4104-9675-1432af42bc62","decision":"publish","abstract":"The gopher tortoise (Gopherus polyphemus) is listed in the State of Florida as a threatened species. It is well known that the microbiota of the host is imperative to health promotion and disease mitigation. The diversity of the gut microbiota of the tortoise has not been extensively surveyed. In this study, we examined both the bacterial and fungal diversity in the fecal material of this animal using bacterial tag-encoded flexible-Titanium (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded FLX amplicon pyrosequencing. In the six samples, there were 16 total bacterial phyla identified with Bacillota (54.55 to 86.13%) as the most dominant and two fungal phyla identified with Ascomycota (79.64 to 97.32%) as the most predominant. Interestingly, the pathogenic fungus Candida tropicalis was detected in all samples suggesting the tortoise could be a reservoir of zoonotic fungi.
","acknowledgements":"This research was done as part of a High Honors project under the leadership of Matthew Janisin, Executive Vice-President (EVP). We thank Maxwell Banor, Nicole Dutton and Donald Zakutansky for their enthusiastic support of this research. We thank Tricia LaPointe, executive director, and Valerie Wolfrey, curator, at the Peace River Wildlife Center (PRWC). We also thank Kellie Reitzel for placing us in contact with members of the PRWC.
","authors":[{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["methodology","writing_originalDraft","writing_reviewEditing"],"email":"vankonil1@mail.gtc.edu","firstName":"Lauren M.K.","lastName":"Vankoningsveld","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["conceptualization","fundingAcquisition","writing_originalDraft","writing_reviewEditing"],"email":"mclaughlinr@gtc.edu","firstName":"Richard W.","lastName":"McLaughlin","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-4634-7096"},{"affiliations":["Gateway Technical College, Kenosha, Wisconsin, United States"],"departments":["School of Liberal Arts and Sciences"],"credit":["investigation","methodology","writing_originalDraft"],"email":"bevisd@gtc.edu","firstName":"Durward L.","lastName":"Bevis","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/f9ef6d9e5d313a8ed83849c831e5b0e6.csv"},"extendedData":[],"funding":"This project was supported by funding provided by Gateway Technical College and by the Gateway Foundation.
","image":{"url":null},"imageCaption":"An analysis of the Predicted Bacterial Phyla (1A), Predicted Bacterial Genera (1B), Bacterial Information (1C), Predicted Fungal Phyla (1D), Predicted Fungal Genera (1E), and Fungal Information (1F). The values listed in sections 1A, 1B, 1D, and 1E represent a relative percentage of zero-radius operational taxonomic units (ZOTUs).
","imageTitle":"
Bacterial and fungal diversity present in the fecal material of two gopher tortoises
","methods":"Animals and sample collection
The two gopher tortoises in this study live at the Peace River Wildlife Center Punta Gorda, Florida. Ruffles is a 61-year-old female, with severe metabolic bone disease (MBD) from many years of incorrect husbandry which has resulted in a disfigured shell. The shell length is 9 inches. Legolas is a female of unknown age with a shell length of 14.5 inches. Three samples from each tortoise were collected over an approximate one-month period of time and placed into separate containers. The date of sampling is found in Table 1. All samples were transported and then stored in a − 40 °C freezer until used.
Microbiota analysis
The bacterial diversity and the fungal diversity within the six-gopher tortoise fecal samples used for our study were determined using bTEFAP® services. These assays were performed by MR DNA (Shallowater, TX). Primers 515F-806 (forward: GAG TTT GAT CNT GGC TCA G;
reverse: GTN TTA CNG CGG CKG CTG) and ITS1-2 (forward: CTT GGT CAT TTA GAG GAA GTA A; reverse: GCT GCG TTC TTC ATC GAT GC) were used to amplify bacterial and fungal DNA, respectively. A more detailed explanation of the methods can be found in the study by Sanchez et al., 2021.
","reagents":"","patternDescription":"Gopher tortoises (Gopherus polyphemus) are mostly found in the Southeastern United States and along the Coastal Plains. Gopher tortoises are listed as a threatened species by the State of Florida (Florida Fish and Wildlife Commission, 2025). These animals often burrow in dry sandy environments (Florida Fish and Wildlife Commission, 2025). However, they are subjected to numerous problems including habitat degradation and forced relocation. This can result in an unnatural mixing of the populations and an increased exposure to harmful parasites and disease (Huffman et al., 2018; Cozad et al., 2020; Folt et al., 2022; Whitfield et al., 2024; Jones et al., 2025).
The diet of many tortoise species generally includes flowers, fruit, legumes, and several varieties of grass. (Abella and Berry, 2016; Figueroa et al., 2024). Though the diet of tortoises is well known, the information regarding the gut microbiome is lacking, which is not uncommon for reptilian herbivores (Sandri et al., 2020). This scarcity of information limits our understanding of the disease process and resilience of the animal.
In this current study amplicon sequencing was performed to obtain an inventory of the bacterial and fungal diversity in the fecal material of two gopher tortoises, Ruffles and Legolas, living at the Peace River Wildlife Center in Punta Gorda, Florida. As a noninvasive technique, fecal samples are often utilized to examine the gut microbiome of animals (Tang et al., 2020). Three samples from each tortoise were collected over a one-month period of time. The average number of sequences and ZOTUs for Ruffles’ bacterial diversity was 29429 and 402, respectively. The average number of sequences and ZOTUs for Legolas’ bacterial diversity was 29442 and 410, respectively. The most abundant bacterial phylum in all samples was Bacillota (formerly Firmicutes), followed by Pseudomonadota (formerly Proteobacteria). The most predominant genus found in four of the samples was Clostridium (Table 1).
In terms of fungi, the average number of sequences and ZOTUs for Ruffles was 28107 and 185, respectively. The average number of sequences and ZOTUs for Legolas was 29200 and 183, respectively. The most abundant fungal phylum throughout the samples was Ascomycota. Candida was the most abundant genera in four of the six samples (Table 1).
Amplicon sequencing has been used to assess the fecal microbiome in different tortoise species. In the Seychelles giant tortoises (Aldabrachelys gigantea) living in different environments the most abundant phyla were Bacteroidota (42.00%), Bacillota (32.00%), and Spirochaetota (9.00%) (Sandri et al., 2020). In desert tortoises Bacillota, Bacteroidota, and Actinobacteroidota comprised the majority of the phyla found in the samples (Blair et al., 2025). In captive Bolson tortoises (Gopherus flavomarginatus) the most abundant phylum was Bacillota followed by Fibrobacterota (García-De La Peña et al., 2019). In a previous study examining the bacterial diversity in the fecal material of a south-central Florida population of gopher tortoises, the most predominant phyla were the Bacillota (36.00%) and Bacteroidetes (36.50%) (Yang et al., 2015). In a more recent study examining a population living in Abacoa Greenway in Jupiter, Florida, 20 different phyla were identified with Bacillota (70.44%) as the most predominant (Giakoumas et al., 2024). In our study, the average percentage of Bacillota for Ruffles was 70.35, and for Legalos was 71.60 which is much higher than detected in the study completed by Yang et al., (2015), but very similar to the results found in the study Giakoumas et al., (2024). Our findings were more consistent with those of previous studies conducted on herbivorous reptiles. For example, in the Galapagos tortoise (Chelonoidis nigra), the green iguana (Iguana iguana), and the marine iguana (Amblyrhynchus cristatus) the relative abundance of Bacillota was 81.10%, 74.00% and 75.10%, respectively (Hong et al., 2011).
In our study, in terms of fungal diversity there were only two phyla present, Ascomycota and Basidiomycota (Table 1). In previous gopher tortoise studies, the fungal diversity was not examined. It has been documented that in the fecal material of reptiles these two phyla are seldomly found (Weber, 1970). Ascomycota and Basidiomycota are major decomposers of plant cell walls. Specifically, Ascomycetes are primarily responsible for the digestion of cellulose and hemicellulose, whereas Basidiomycetes are more active in lignin degradation (Manici et al., 2024). These fungi are commonly detected in the gastrointestinal tracts of animals and often dominate the gut mycobiota, particularly in herbivores consuming a plant-rich diet (Zhao et al., 2023; Lv et al., 2023).
The breakdown of dietary cellulose and hemicellulose can also be accomplished by cellulolytic bacteria. Many such bacteria that are found within the phyla Bacillota as well as Bacteroidetes are capable of cellulose digestion (Bhatia et al., 2024). The gopher tortoise is a hindgut fermenter that utilizes microbial fermentation of starch in the hindgut. Unnamed bacterial taxa likely play an important role in the metabolism of the animal and warrant further investigation (Giakoumas et al., 2024). However, this is also likely true of the fungal taxa.
Finally, it is well known animals can be reservoirs for pathogens. In a previous study involving gopher tortoises the potential pathogens Mycoplasmaceae sp., and Helicobacter sp. were detected (Giakoumas et al., 2024). These bacterial species were not detected in this current study. In our study we detected Candida tropicalis with a range of 1.41–75.00% of the sequences for Ruffles and 2.31-92.20% of the sequences for Legolas. This zoonotic fungal species has been detected in the Puff adder (Bitis arietans), the Moroccan cobra (Naja haje legionis) (Ugochukwu et al., 2024), bats (Pinto et al., 2025), cetaceans (Garcia-Bustos et al., 2024), cows (Clarke, 1960), goats, sheep, psittacines, rhea monkeys, horses, sirenians, and shrimp (Cordeiro Rde et al., 2014). This yeast can cause mastitis in cows (Clarke, 1960), blood stream infections in humans (Guinea, 2014) and oropharyngeal candidiasis (Collins et al., 2011). In conclusion, our study reaffirms the role of animals as reservoirs for zoonotic microorganisms. These findings underscore the importance of continued surveillance of microbial communities in animals to better understand pathogen distribution and potential risks to human health.
","references":[{"reference":"Abella SR, Berry KH. 2016. Enhancing and Restoring Habitat for the Desert Tortoise. Journal of Fish and Wildlife Management 7: 255-279.
","pubmedId":"","doi":"10.3996/052015-JFWM-046"},{"reference":"Bhatia T, Bose D, Sharma D, Patel D. 2024. A Review on Cellulose Degrading Microbes and its Applications. Industrial Biotechnology 20: 26-39.
","pubmedId":"","doi":"10.1089/ind.2023.0025"},{"reference":"Blair EM, Margalith NJ, O’Malley MA. 2025. Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota. Microbial Ecology 88: 10.1007/s00248-025-02557-6.
","pubmedId":"","doi":"10.1007/s00248-025-02557-6"},{"reference":"Clarke RTJ. 1960. Rumen Candida species and bovine mastitis. New Zealand Veterinary Journal 8: 79-79.
","pubmedId":"","doi":"10.1080/00480169.1960.33385"},{"reference":"Collins CD, Cookinham S, Smith J. 2011. Management of oropharyngeal candidiasis with localized oral miconazole therapy: efficacy, safety, and patient acceptability. Patient Prefer Adherence 5: 369-74.
","pubmedId":"21845036","doi":"10.2147/PPA.S14047"},{"reference":"Cordeiro Rde A, de Oliveira JS, Castelo-Branco Dde S, Teixeira CE, Marques FJ, Bittencourt PV, et al., Rocha MF. 2015. Candida tropicalis isolates obtained from veterinary sources show resistance to azoles and produce virulence factors. Med Mycol 53(2): 145-52.
","pubmedId":"25550392","doi":""},{"reference":"Cozad RA, Hernandez SM, Norton TM, Tuberville TD, Stacy NI, Stedman NL, Aresco MJ. 2020. Epidemiological Investigation of a Mortality Event in a Translocated Gopher Tortoise (Gopherus polyphemus) Population in Northwest Florida. Front Vet Sci 7: 120.
","pubmedId":"32211432","doi":""},{"reference":"Florida Fish and Wildlife Commission [FFWC] Gopher Tortoise Management Plan. Florida Fish and Wildlife Commission; Tallahassee, FL, USA: 2024. [(accessed on 15 July 2025)]. Available online: https://myfwc.com/media/xd1icqci/gtmgmtplan2024.pdf
","pubmedId":"","doi":""},{"reference":"Figueroa A, Coblentz K, Herrera A, Cuni L, Villate J, Liu H, Araujo MS, Whitfield SM. 2024. Seasonal Frugivory Facilitates Individual Diet Specialization in the Generalist Herbivore Gopher Tortoise. : 10.2139/ssrn.4822385.
","pubmedId":"","doi":"10.2139/ssrn.4822385"},{"reference":"Folt B, Marshall M, Emanuel JA, Dziadzio M, Cooke J, Mena L, et al., McGowan. 2022. Using predictions from multiple anthropogenic threats to estimate future population persistence of an imperiled species. Global Ecology and Conservation 36: e02143.
","pubmedId":"","doi":"10.1016/j.gecco.2022.e02143"},{"reference":"Garcia-Bustos V, Acosta-Hernández B, Cabañero-Navalón MD, Ruiz-Gaitán AC, Pemán J, Rosario Medina I. 2024. Potential Fungal Zoonotic Pathogens in Cetaceans: An Emerging Concern. Microorganisms 12(3): 10.3390/microorganisms12030554.
","pubmedId":"38543604","doi":""},{"reference":"García-De La Peña C, Garduño-Niño E, Vaca-Paniagua F, Díaz-Velásquez C, Barrows CW, Gomez-Gil B, Valenzuela-Núñez, LM. 2019. Comparison of the fecal bacterial microbiota composition between wild and captive bolson tortoises (Gopherus flavomarginatus). Herpetol Conserv Bio 14 :587–600.
","pubmedId":"","doi":""},{"reference":"Giakoumas DS, Moore J, Stamper E, Bernot KM, Mincer TJ. 2024. State-threatened gopher tortoise (Gopherus polyphemus) gut microbiome analysis reveals health insights into southeastern Florida population. BioRxiv.
","pubmedId":"","doi":""},{"reference":"Guinea J. 2014. Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect 20 Suppl 6: 5-10.
","pubmedId":"24506442","doi":""},{"reference":"Hong PY, Wheeler E, Cann IK, Mackie RI. 2011. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. ISME J 5(9): 1461-70.
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","pubmedId":"39341972","doi":""},{"reference":"Webster J. 1970. Coprophilous fungi. Transactions of the British Mycological Society 54: 161-180.
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Predicted Bacterial Phyla":"Basidiomycota","Ruffles 3/18/25":"3.61","Ruffles 3/26/25":"10.11","Ruffles 4/20/25":"20.36","Legolas 3/19/25":"6.34","Legolas 3/25/25":"2.68","Legolas 4/18/25":"8.52"},{" 1A. Predicted Bacterial Phyla":"Ascomycota","Ruffles 3/18/25":"96.39","Ruffles 3/26/25":"89.89","Ruffles 4/20/25":"79.64","Legolas 3/19/25":"93.66","Legolas 3/25/25":"97.32","Legolas 4/18/25":"91.48"},{" 1A. Predicted Bacterial Phyla":"1E. Abundant Predicted Fungal Genera","Ruffles 3/18/25":"Ruffles 3/18/25","Ruffles 3/26/25":"Ruffles 3/26/25","Ruffles 4/20/25":"Ruffles 4/20/25","Legolas 3/19/25":"Legolas 3/19/25","Legolas 3/25/25":"Legolas 3/25/25","Legolas 4/18/25":"Legolas 4/18/25"},{" 1A. Predicted Bacterial Phyla":"Candida","Ruffles 3/18/25":"1.55","Ruffles 3/26/25":"75.16","Ruffles 4/20/25":"21.71","Legolas 3/19/25":"2.50","Legolas 3/25/25":"92.28","Legolas 4/18/25":"67.81"},{" 1A. Predicted Bacterial Phyla":"Phaeosphaeria","Ruffles 3/18/25":"8.08","Ruffles 3/26/25":"2.57","Ruffles 4/20/25":"6.77","Legolas 3/19/25":"13.72","Legolas 3/25/25":"0.71","Legolas 4/18/25":"5.11"},{" 1A. Predicted Bacterial Phyla":"Parasarocladium","Ruffles 3/18/25":"54.04","Ruffles 3/26/25":"1.14","Ruffles 4/20/25":"1.45","Legolas 3/19/25":"5.96","Legolas 3/25/25":"0.93","Legolas 4/18/25":"1.26"},{" 1A. Predicted Bacterial Phyla":"Paraconiothyrium","Ruffles 3/18/25":"5.78","Ruffles 3/26/25":"1.74","Ruffles 4/20/25":"7.34","Legolas 3/19/25":"10.54","Legolas 3/25/25":"0.68","Legolas 4/18/25":"3.72"},{" 1A. Predicted Bacterial Phyla":"Cladosporium","Ruffles 3/18/25":"4.52","Ruffles 3/26/25":"1.01","Ruffles 4/20/25":"5.07","Legolas 3/19/25":"8.45","Legolas 3/25/25":"0.36","Legolas 4/18/25":"2.34"},{" 1A. Predicted Bacterial Phyla":"Agaricus","Ruffles 3/18/25":"1.62","Ruffles 3/26/25":"8.54","Ruffles 4/20/25":"18.42","Legolas 3/19/25":"2.40","Legolas 3/25/25":"2.27","Legolas 4/18/25":"5.82"},{" 1A. Predicted Bacterial Phyla":"Alfaria","Ruffles 3/18/25":"2.30","Ruffles 3/26/25":"0.71","Ruffles 4/20/25":"1.71","Legolas 3/19/25":"12.57","Legolas 3/25/25":"0.22","Legolas 4/18/25":"3.04"},{" 1A. Predicted Bacterial Phyla":"Pestalotiopsis","Ruffles 3/18/25":"1.66","Ruffles 3/26/25":"2.77","Ruffles 4/20/25":"8.98","Legolas 3/19/25":"2.87","Legolas 3/25/25":"0.33","Legolas 4/18/25":"1.75"},{" 1A. Predicted Bacterial Phyla":"1F. Fungal Information","Ruffles 3/18/25":"Ruffles 3/18/25","Ruffles 3/26/25":"Ruffles 3/26/25","Ruffles 4/20/25":"Ruffles 4/20/25","Legolas 3/19/25":"Legolas 3/19/25","Legolas 3/25/25":"Legolas 3/25/25","Legolas 4/18/25":"Legolas 4/18/25"},{" 1A. Predicted Bacterial Phyla":"Number of Sequences ","Ruffles 3/18/25":"32395","Ruffles 3/26/25":"23967","Ruffles 4/20/25":"27958","Legolas 3/19/25":"28265","Legolas 3/25/25":"33941","Legolas 4/18/25":"25394"},{" 1A. Predicted Bacterial Phyla":"Average Number of Sequences","Ruffles 3/18/25":".","Ruffles 3/26/25":"28107","Ruffles 4/20/25":".","Legolas 3/19/25":".","Legolas 3/25/25":"29200","Legolas 4/18/25":"."},{" 1A. Predicted Bacterial Phyla":"Number of ZOTUs","Ruffles 3/18/25":"197","Ruffles 3/26/25":"171","Ruffles 4/20/25":"186","Legolas 3/19/25":"206","Legolas 3/25/25":"156","Legolas 4/18/25":"186"},{" 1A. Predicted Bacterial Phyla":"Average Number of ZOTUs","Ruffles 3/18/25":".","Ruffles 3/26/25":"185","Ruffles 4/20/25":".","Legolas 3/19/25":".","Legolas 3/25/25":"183","Legolas 4/18/25":"."}]}}}, "staticQueryHashes": ["2114697108"]}