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Ettinger CL, Wu-Woods J, Kurbessoian T, Brown DJ, de Souza Pacheco I, Vindiola BG, Walling LL, Atkinson PW, Byrne FJ, Redak R, Stajich JE. Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters. mSphere 2023; 8:e0026723. [PMID: 37800904 PMCID: PMC10597469 DOI: 10.1128/msphere.00267-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/24/2023] [Indexed: 10/07/2023] Open
Abstract
The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, Xylella fastidiosa, resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.
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Affiliation(s)
- Cassandra L. Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Jessica Wu-Woods
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Tania Kurbessoian
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Dylan J. Brown
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | | | - Beatriz G. Vindiola
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Linda L. Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Peter W. Atkinson
- Department of Entomology, University of California, Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Frank J. Byrne
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Richard Redak
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
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Yue R, Chen H, Xu X, Xia Y, Sun Y, Xia M, Xia D, Sun B. Maternal and infantile gut mycobiome during the weaning period in free ranging Tibetan macaques ( Macaca thibetana). Ecol Evol 2023; 13:e10108. [PMID: 37214608 PMCID: PMC10196218 DOI: 10.1002/ece3.10108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Gut microbiome is critical to the health of mammals. Many previous studies have revealed the gut bacterial microbiomes of mother and infant changed significantly during the weaning period. However, little is known concerning the gut mycobiome of wild primates. Here, we examined the variations on gut mycobiome between weaning and post-weaning for both mother and infant in wild-living Tibetan macaques (Macaca thibetana). Our results showed that the gut mycobiomes of mother and infant were dominated by two phyla Ascomycota and Basidiomycota. For both mother and infant, the ASV richness of gut mycobiome remained relatively steady from weaning to post-weaning periods, while the Shannon indexes increased significant in weaning compared to post-weaning periods. However, no significant difference between mother and infant ASV richness and Shannon indexes during weaning and post-weaning periods respectively. Compared to mothers, we found that much more known taxa of gut fungi were enriched in weaning or post-weaning periods of infants. In particular, we found that the dominant genus Aspergillus was enriched in infants during weaning period. Furthermore, we found that the relative abundance of plant pathogens were significantly higher in the post-weaning period than in the weaning period for infants. Our results indicated that weaning events could affect the gut mycobiome significantly for both mothers and infant in Tibetan macaques, which had a stronger effect on the gut mycobiome of infant monkeys than on their mothers.
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Affiliation(s)
- Ran Yue
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Huijuan Chen
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Xiaojuan Xu
- School of Life SciencesHefei Normal UniversityHefeiChina
| | - Yingna Xia
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Yu Sun
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Mengyi Xia
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Dongpo Xia
- School of Life SciencesAnhui UniversityHefeiChina
| | - Binghua Sun
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
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3
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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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4
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Turunen J, Paalanne N, Reunanen J, Tapiainen T, Tejesvi MV. Development of gut mycobiome in infants and young children: a prospective cohort study. Pediatr Res 2023:10.1038/s41390-023-02471-y. [PMID: 36670159 PMCID: PMC10382308 DOI: 10.1038/s41390-023-02471-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/21/2022] [Accepted: 01/01/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND The composition of the gut fungal microbiome, mycobiome, is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants and children. Here we investigate how perinatal events influence the development of gut mycobiome. METHODS In this prospective cohort study of 140 infants, we used ITS gene sequencing of fecal samples from birth to the age of 18 months. We compared gut mycobiome composition according to delivery mode and exposure to intrapartum antibiotics during vaginal delivery. RESULTS At birth, gut mycobiome were dominated by the genus Candida, at 6-month stool samples by Malassezia and Cystofilobasidium, and the 18-month stool samples by Trichosporon and unidentified fungi. Perinatal factors altered mycobiome. At 18 months, gut mycobiome of infants born vaginally consisted mostly of Trichosporon (32%) and unidentified fungi (31%), while those born via Cesarean section delivery samples had mycobiome dominated by Saccharomyces (50%). At the age of 18 months, those exposed to intrapartum antibiotics had mycobiome dominated by Trichosporon (66%) not seen in those unexposed to antibiotics. CONCLUSIONS Delivery mode and exposure to intrapartum antibiotic prophylaxis were markedly associated with gut mycobiome composition from birth to 18 months of age. IMPACT The composition of the gut mycobiome is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants and children. In this prospective cohort study, delivery mode and exposure to intrapartum antibiotic prophylaxis were markedly associated with gut mycobiome composition from birth to 18 months of age. The impact of intrapartum antibiotic prophylaxis on fungal microbiome in vaginally born infants, previously shown to influence gut bacteriome composition, may be explained by the interaction between bacteria and fungi. Gut mycobiome composition likely deserves further investigation in relation to gut microbiome and health in children.
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Affiliation(s)
- Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland. .,Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Mysore V Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
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5
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Worsley SF, Davies CS, Mannarelli ME, Komdeur J, Dugdale HL, Richardson DS. Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler. MICROBIOME 2022; 10:242. [PMID: 36575553 PMCID: PMC9795730 DOI: 10.1186/s40168-022-01432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fungi, are notably lacking, despite their potential to influence host processes. Here, we characterise the fungal GM of individuals living in a natural population of Seychelles warblers (Acrocephalus sechellensis). We evaluate the extent to which fungal GM structure is shaped by environment and host factors, including genome-wide heterozygosity and variation at key immune genes (major histocompatibility complex (MHC) and Toll-like receptor (TLR)). Importantly, we also explore the relationship between fungal GM differences and subsequent host survival. To our knowledge, this is the first time that the genetic drivers and fitness consequences of fungal GM variation have been characterised for a wild vertebrate population. RESULTS Environmental factors, including season and territory quality, explain the largest proportion of variance in the fungal GM. In contrast, neither host age, sex, genome-wide heterozygosity, nor TLR3 genotype was associated with fungal GM differences in Seychelles warblers. However, the presence of four MHC-I alleles and one MHC-II allele was associated with changes in fungal GM alpha diversity. Changes in fungal richness ranged from between 1 and 10 sequencing variants lost or gained; in some cases, this accounted for 20% of the fungal variants carried by an individual. In addition to this, overall MHC-I allelic diversity was associated with small, but potentially important, changes in fungal GM composition. This is evidenced by the fact that fungal GM composition differed between individuals that survived or died within 7 months of being sampled. CONCLUSIONS Our results suggest that environmental factors play a primary role in shaping the fungal GM, but that components of the host immune system-specifically the MHC-may also contribute to the variation in fungal communities across individuals within wild populations. Furthermore, variation in the fungal GM can be associated with differential survival in the wild. Further work is needed to establish the causality of such relationships and, thus, the extent to which components of the GM may impact host evolution. Video Abstract.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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6
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Xia Y, Xu X, Chen H, Yue R, Xia D, Wang X, Li J, Sun B. Effects of captive and primate-focused tourism on the gut microbiome of Tibetan macaques. Front Microbiol 2022; 13:1023898. [PMID: 36312969 PMCID: PMC9607900 DOI: 10.3389/fmicb.2022.1023898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
Documenting the effects of anthropogenic activities on the gut microbiome of wild animals is important to their conservation practices. Captivity and ecotourism are generally considered two common anthropogenic disturbances on the health of nonhuman primates. Here, we examined the divergences of gut microbiome in different environments of Tibetan macaques. Our results showed that there were no significant differences in the alpha diversity, predominant families and genera of gut microbiomes between wild and tourist groups. However, these indexes decreased significantly in the captive individuals. In addition, the significant differences of beta diversity and community compositions between wild and tourism groups also were detected. In particular, higher potential pathogenic and predicted KEGG pathway of drug resistance (antimicrobial) were detected in the gut microbiome of individuals in captive environment. Our results indicated that living in the wild are beneficial to maintaining gut microbial diversity of Tibetan macaques, while captivity environment is harmful to the health of this macaque. Exploring ways to restore the native gut microbiome and its diversity of captive individual should pay more attention to in the future studies.
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Affiliation(s)
- Yingna Xia
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Xiaojuan Xu
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Huijuan Chen
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Ran Yue
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Dongpo Xia
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
- School of Life Sciences, Anhui University, Hefei, China
| | - Xi Wang
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Jinhua Li
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
- School of Life Sciences, Hefei Normal University, Hefei, China
- *Correspondence: Jinhua Li,
| | - Binghua Sun
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
- Binghua Sun,
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7
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Kuthyar S, Watson K, Huang S, Brent LJN, Platt M, Horvath J, Gonzalez-Martinez J, Martínez M, Godoy-Vitorino F, Knight R, Dominguez-Bello MG, Amato KR. Limited microbiome differences in captive and semi-wild primate populations consuming similar diets. FEMS Microbiol Ecol 2022; 98:fiac098. [PMID: 36047944 PMCID: PMC9528791 DOI: 10.1093/femsec/fiac098] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Gut microbial communities are shaped by a myriad of extrinsic factors, including diet and the environment. Although distinct human populations consistently exhibit different gut microbiome compositions, variation in diet and environmental factors are almost always coupled, making it difficult to disentangle their relative contributions to shaping the gut microbiota. Data from discrete animal populations with similar diets can help reduce confounds. Here, we assessed the gut microbiota of free-ranging and captive rhesus macaques with at least 80% diet similarity to test the hypothesis that hosts in difference environments will have different gut microbiomes despite a shared diet. Although we found that location was a significant predictor of gut microbial composition, the magnitude of observed differences was relatively small. These patterns suggest that a shared diet may limit the typical influence of environmental microbial exposure on the gut microbiota.
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Affiliation(s)
- Sahana Kuthyar
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
- Division of Biological Sciences, University of California San Diego 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Karli Watson
- Institute of Cognitive Science, University of Colorado Boulder 1777 Exposition Drive Boulder, CO, 80309, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter Stocker Rd, Exeter EX4 4PY, United Kingdom
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd Philadelphia, PA, 19104, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, 425 S. University Ave Philadelphia, PA, 19104-6018, USA
- Department of Marketing, Wharton School of Business, University of Pennsylvania, 3620 Locust Walk, Philadelphia, PA, USA 19104, PA, USA
| | - Julie Horvath
- Research and Collections, North Carolina Museum of Natural Sciences, 11 W Jones St, Raleigh, NC, 27601, USA
- Biological and Biomedical Sciences Department, North Carolina Central University, 1801 Fayetteville St, Durham, NC, 27707, USA
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Campus Box 90383 Durham, NC, 27708, USA
- Department of Biological Sciences, North Carolina State University, 3510 Thomas Hall Campus Box 7614 Raleigh, NC, USA 27695, USA
| | - Janis Gonzalez-Martinez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Melween Martínez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, Medical Sciences Campus, PO BOX 365067 San Juan, PR 00936-5067, Puerto Rico
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
- Department of Computer Sciences and Engineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, USA 08901, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA 1810, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
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8
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Xu X, Xia Y, Sun B. Linking the bacterial microbiome between gut and habitat soil of Tibetan macaque ( Macaca thibetana). Ecol Evol 2022; 12:e9227. [PMID: 36177115 PMCID: PMC9471045 DOI: 10.1002/ece3.9227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Soil is a part of the habitat environment of terrestrial or semi‐terrestrial mammals, which contains a wide variety of microbes. Although the soil microbiome of the host habitat is considered to be a potentially important influence factor on the mammalian gut microbiome and health, few data are currently available to explore the relationship between gut and host habitat soil microbiome in wild primates. Here, marked divergence of the bacterial microbiome in composition and structure between Tibetan macaques (Macaca thibetana) guts and its habitat soil were detected. In addition, we found that most of the core genera abundance and ASVs in the Tibetan macaques' gut bacterial microbiome could be detected in the corresponding soil samples, but with low abundance. However, the core abundant genera abundant in soil are almost undetectable in the gut of Tibetan macaques. Although there are some ASVs shared by gut and soil bacterial microbiome, the abundant shared ASVs in the guts of Tibetan macaques were rare bacterial taxa in the corresponding soil samples. Notably, all the ASVs shared by guts and soil were present in the soil at relatively low abundance, whereas they were affiliated with diverse bacterial taxa. By linking the bacterial microbiome between Tibetan macaques’ gut and its habitat soil, our findings suggest that the predominant bacterial groups from the soil were not likely to colonize the Tibetan macaques' gut, whereas the low‐abundance but diverse soil bacteria could be selected by the gut. Whether these rare and low‐abundant bacteria are permanent residents of the soil or a source of fecal contamination remains to be determined in future study.
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Affiliation(s)
- Xiaojuan Xu
- School of Life Science Hefei Normal University Hefei China
| | - Yingna Xia
- School of Resource and Environmental Engineering Anhui University Hefei China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology Anhui University Hefei China
| | - Binghua Sun
- School of Resource and Environmental Engineering Anhui University Hefei China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology Anhui University Hefei China
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9
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Hu J, Wei S, Gu Y, Wang Y, Feng Y, Sheng J, Hu L, Gu C, Jiang P, Tian Y, Guo W, Lv L, Liu F, Zou Y, Yan F, Feng N. Gut Mycobiome in Patients With Chronic Kidney Disease Was Altered and Associated With Immunological Profiles. Front Immunol 2022; 13:843695. [PMID: 35784313 PMCID: PMC9245424 DOI: 10.3389/fimmu.2022.843695] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Mounting evidence suggests that bacterial dysbiosis and immunity disorder are associated with patients with chronic kidney disease (CKD), but the mycobiome is beginning to gain recognition as a fundamental part of our microbiome. We aim to characterize the profile of the mycobiome in the gut of CKD patients and its correlation to serum immunological profiles. Methods and materials Ninety-two CKD patients and sex-age-body mass index (BMI)-matched healthy controls (HCs) were recruited. Fresh samples were collected using sterile containers. ITS transcribed spacer ribosomal RNA gene sequencing was performed on the samples. An immunoturbidimetric test was used to assess the serum levels of immunological features. Results The CKD cohort displayed a different microbial community from that in the HC cohort according to principal coordinate analysis (PCoA). (P=0.001). The comparison of the two cohorts showed that the CKD cohort had significantly higher gut microbial richness and diversity (P<0.05). The CKD cohort had lower abundances of Candida, Bjerkandera, Rhodotorula, and Ganoderma compared to the HC cohort, while it had higher Saccharomyces (P<0.05). However, the microbial community alteration was inconsistent with the severity of kidney damage in patients, as only patients in CKD stage 1~3 had differed microbial community concerning for HCs based on PCoA (P<0.05). The serum concentration of the kappa light chain in CKD patients was positively associated with Saccharomyces, whereas the it was negatively associated with Ganoderma (P<0.05). Conclusions Not only was gut mycobiome dysbiosis observed in CKD patients, but the dysbiosis was also associated with the immunological disorder. These findings suggest that therapeutic strategies targeting gut mycobiome might be effective.
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Affiliation(s)
- Jialin Hu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Shichao Wei
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Yifeng Gu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yang Wang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Yangkun Feng
- School of Medicine, Nantong University, Nantong, China
| | - Jiayi Sheng
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Lei Hu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Chaoqun Gu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Peng Jiang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Yu Tian
- Department of Nephrology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Wei Guo
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Longxian Lv
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yeqing Zou
- School of Basic Medicine, Jiangsu Vocational College of Medicine, Yancheng, China
| | - Feng Yan
- Department of Nephrology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
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10
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Weinstein SB, Stephens WZ, Greenhalgh R, Round JL, Dearing MD. Wild herbivorous mammals (genus Neotoma) host a diverse but transient assemblage of fungi. Symbiosis 2022; 87:45-58. [PMID: 37915425 PMCID: PMC10619970 DOI: 10.1007/s13199-022-00853-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/14/2022] [Indexed: 10/16/2022]
Abstract
Fungi are often overlooked in microbiome research and, as a result, little is known about the mammalian mycobiome. Although frequently detected in vertebrate guts and known to contribute to digestion in some herbivores, whether these eukaryotes are a persistent part of the mammalian gut microbiome remains contentious. To address this question, we sampled fungi from wild woodrats (Neotoma spp.) collected from 25 populations across the southwestern United States. For each animal, we collected a fecal sample in the wild, and then re-sampled the same individual after a month in captivity on a controlled diet. We characterized and quantified fungi using three techniques: ITS metabarcoding, shotgun metagenomics and qPCR. Wild individuals contained diverse fungal assemblages dominated by plant pathogens, widespread molds, and coprophilous taxa primarily in Ascomycota and Mucoromycota. Fungal abundance, diversity and composition differed between individuals, and was primarily influenced by animal geographic origin. Fungal abundance and diversity significantly declined in captivity, indicating that most fungi in wild hosts came from diet and environmental exposure. While this suggests that these mammals lack a persistent gut mycobiome, natural fungal exposure may still impact fungal dispersal and animal health.
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Affiliation(s)
- Sara B. Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - W. Zac Stephens
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT, USA
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - June L. Round
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT, USA
| | - M. Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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11
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Sharma AK, Davison S, Pafco B, Clayton JB, Rothman JM, McLennan MR, Cibot M, Fuh T, Vodicka R, Robinson CJ, Petrzelkova K, Gomez A. The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors. NPJ Biofilms Microbiomes 2022; 8:12. [PMID: 35301322 PMCID: PMC8930997 DOI: 10.1038/s41522-022-00274-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.
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Affiliation(s)
- Ashok K Sharma
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA.,Department of Gastroenterology, Inflammatory Bowel & Immunology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Sam Davison
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA.,Callitrichid Research Center (CRC, Marmoset Colony) at the University of Nebraska at Omaha, Omaha, NE, USA.,Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, USA.,New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Matthew R McLennan
- Department of Social Sciences, Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK.,Bulindi Chimpanzee & Community Project, Hoima, Uganda
| | - Marie Cibot
- Department of Social Sciences, Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK.,Bulindi Chimpanzee & Community Project, Hoima, Uganda.,Anicoon Vétérinaires, Ploemeur, France
| | - Terence Fuh
- WWF Central African Republic, Bayanga, Central African Republic
| | | | | | - Klara Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Brno, Czech Republic
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA. .,Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA.
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12
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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13
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Xi L, Qin X, Song Y, Han J, Li Z, Zhang J. Gut Microbial Alterations in Diarrheal Baer's Pochards ( Aythya baeri). Front Vet Sci 2021; 8:756486. [PMID: 34722711 PMCID: PMC8551490 DOI: 10.3389/fvets.2021.756486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/03/2021] [Indexed: 01/07/2023] Open
Abstract
The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.
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Affiliation(s)
- Li Xi
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China.,Henan Engineering Research Center of Development and Application of Green Feed Additives, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Xinxi Qin
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Yumin Song
- Linyi Agricultural Science and Technology Career Academy, Linyi, China
| | - Jincheng Han
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China.,Henan Engineering Research Center of Development and Application of Green Feed Additives, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Zhiqiang Li
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China.,Henan Engineering Research Center of Development and Application of Green Feed Additives, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Jinliang Zhang
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China.,Henan Engineering Research Center of Development and Application of Green Feed Additives, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
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14
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Sun B, Xia Y, Davison S, Gomez A, Garber PA, Amato KR, Xu X, Xia DP, Wang X, Li JH. Assessing the Influence of Environmental Sources on the Gut Mycobiome of Tibetan Macaques. Front Microbiol 2021; 12:730477. [PMID: 34421885 PMCID: PMC8372991 DOI: 10.3389/fmicb.2021.730477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/09/2021] [Indexed: 12/26/2022] Open
Abstract
The distribution and availability of microbes in the environment has an important effect on the composition of the gut microbiome of wild vertebrates. However, our current knowledge of gut-environmental interactions is based principally on data from the host bacterial microbiome, rather than on links that establish how and where hosts acquire their gut mycobiome. This complex interaction needs to be clarified. Here, we explored the relationship between the gut fungal communities of Tibetan macaques (Macaca thibetana) and the presence of environmental (plant and soil) fungi at two study sites using the fungal internal transcribed spacer (ITS) and next generation sequencing. Our findings demonstrate that the gut, plant and soil fungal communities in their natural habitat were distinct. We found that at both study sites, the core abundant taxa and ASVs (Amplicon Sequence Variants) of Tibetan macaques’ gut mycobiome were present in environmental samples (plant, soil or both). However, the majority of these fungi were characterized by a relatively low abundance in the environment. This pattern implies that the ecology of the gut may select for diverse but rare environmental fungi. Moreover, our data indicates that the gut mycobiome of Tibetan macaques was more similar to the mycobiome of their plant diet than that present in the soil. For example, we found three abundant ASVs (Didymella rosea, Cercospora, and Cladosporium) that were present in the gut and on plants, but not in the soil. Our results highlight a relationship between the gut mycobiome of wild primates and environmental fungi, with plants diets possibly contributing more to seeding the macaque’s gut mycobiome than soil fungi.
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Affiliation(s)
- Binghua Sun
- School of Resource and Environmental Engineering, Anhui University, Hefei, China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Yingna Xia
- School of Resource and Environmental Engineering, Anhui University, Hefei, China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Samuel Davison
- Department of Animal Science, University of Minnesota, St. Paul, MN, United States
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN, United States
| | - Paul A Garber
- Department of Anthropology and Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, United States.,International Centre of Biodiversity and Primate Conservation, Dali University, Dali, China
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, United States
| | - Xiaojuan Xu
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China.,School of Life Sciences, Hefei Normal University, Hefei, China
| | - Dong-Po Xia
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China.,School of Life Sciences, Anhui University, Hefei, China
| | - Xi Wang
- School of Resource and Environmental Engineering, Anhui University, Hefei, China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China
| | - Jin-Hua Li
- School of Resource and Environmental Engineering, Anhui University, Hefei, China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Anhui University, Hefei, China.,School of Life Sciences, Hefei Normal University, Hefei, China
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