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Samartino S, Christie D, Penna A, Sicotte P, Ting N, Wikberg E. Social network dynamics, infant loss, and gut microbiota composition in female Colobus vellerosus during time periods with alpha male challenges. Primates 2024:10.1007/s10329-024-01132-w. [PMID: 38735025 DOI: 10.1007/s10329-024-01132-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/11/2024] [Indexed: 05/13/2024]
Abstract
The gut microbiota of group-living animals is strongly influenced by their social interactions, but it is unclear how it responds to social instability. We investigated whether social instability associated with the arrival of new males and challenges to the alpha male position could explain differences in the gut microbiota in adult female Colobus vellerosus at Boabeng-Fiema, Ghana. First, we used a data set collected during May-August 2007 and May 2008-2009 that consisted of (i) 50 fecal samples from adult females in eight social groups for V4 16S rRNA sequencing to determine gut microbiota composition, and (ii) demographic and behavioral data ad libitum to determine male immigration, challenges to the alpha male position, and infant births and deaths. Sørensen and Bray-Curtis beta diversity indices (i.e., between-sample microbiota variation) were predicted by year, alpha male stability, group identity, and age. Next, we used a more detailed behavioral data set collected during focal observations of adult females in one group with a prolonged alpha male takeover and three cases of infant loss, to create 12-month versus 3-month 1-m proximity networks that preceded and overlapped the gut microbiome sampling period in that group. The long versus short-term networks were not correlated, suggesting temporal variation in proximity networks. In this group, beta diversity among the five adult females was predicted by similarity in infant loss status and short-term (rather than yearly) 1-m proximity ties. Although the mechanism driving this association needs to be further investigated in future studies, our findings indicate that alpha male takeovers are associated with gut microbiota variation and highlight the importance of taking demographic and social network dynamics into account.
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Affiliation(s)
- Shelby Samartino
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Diana Christie
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anna Penna
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Pascale Sicotte
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Eva Wikberg
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
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Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
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Gao H, Jiang F, Zhang J, Chi X, Song P, Li B, Cai Z, Zhang T. Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang). Integr Zool 2023; 18:1089-1104. [PMID: 37231976 DOI: 10.1111/1749-4877.12726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.
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Affiliation(s)
- Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiangwen Chi
- Department of Student Affairs, Qinghai University, Xining, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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Xi L, Han J, Wen X, Zhao L, Qin X, Luo S, Lv D, Song S. Species variations in the gut microbiota of captive snub-nosed monkeys. Front Endocrinol (Lausanne) 2023; 14:1250865. [PMID: 37780618 PMCID: PMC10534982 DOI: 10.3389/fendo.2023.1250865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Snub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments. Methods This study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies. Results The results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function. Discussion In conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.
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Affiliation(s)
- Li Xi
- 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
| | - Jincheng Han
- 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
| | - Xiaohui Wen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Longfei Zhao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Xinxi Qin
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Shengjun Luo
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dianhong Lv
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Xi L, Wen X, Jia T, Han J, Qin X, Zhang Y, Wang Z. Comparative study of the gut microbiota in three captive Rhinopithecus species. BMC Genomics 2023; 24:398. [PMID: 37452294 PMCID: PMC10349479 DOI: 10.1186/s12864-023-09440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Snub-nosed monkeys are highly endangered primates and their population continues to decline with the habitat fragmentation. Artificial feeding and breeding is an important auxiliary conservation strategy. Studies have shown that changes and imbalances in the gut microbiota often cause gastrointestinal problems in captive snub-nosed monkeys. Here, we compare the gut microbiota composition, diversity, and predicted metabolic function of three endangered species of snub-nosed monkeys (Rhinopithecus bieti, R. brelichi, and R. roxellana) under the same captive conditions to further our understanding of the microbiota of these endangered primates and inform captive conservation strategies. 16 S rRNA gene sequencing was performed on fecal samples from 15 individuals (R. bieti N = 5, R. brelichi N = 5, R. roxellana N = 5). RESULTS The results showed that the three Rhinopithecus species shared 24.70% of their amplicon sequence variants (ASVs), indicating that the composition of the gut microbiota varied among the three Rhinopithecus species. The phyla Firmicutes and Bacteroidetes represented 69.74% and 18.45% of the core microbiota. In particular, analysis of microbiota diversity and predicted metabolic function revealed a profound impact of host species on the gut microbiota. At the genus level, significant enrichment of cellulolytic genera including Rikenellaceae RC9 gut group, Ruminococcus, Christensenellaceae R7 group, UCG 004 from Erysipelatoclostridiaceae, and UCG 002 and UCG 005 from Oscillospiraceae, and carbohydrate metabolism including propionate and butyrate metabolic pathways in the gut of R. bieti indicated that R. bieti potentially has a stronger ability to use plant fibers as energy substances. Bacteroides, unclassified Muribaculaceae, Treponema, and unclassified Eubacterium coprostanoligenes group were significantly enriched in R. brelichi. Prevotella 9, unclassified Lachnospiraceae, and unclassified UCG 010 from Oscillospirales UCG 010 were significantly enriched in R. roxellana. Among the predicted secondary metabolic pathways, the glycan biosynthesis and metabolism had significantly higher relative abundance in the gut of R. brelichi and R. roxellana than in the gut of R. bieti. The above results suggest that different Rhinopithecus species may have different strategies for carbohydrate metabolism. The Principal coordinate analysis (PCoA) and Unweighted pair-group method with arithmetic mean (UPGMA) clustering tree revealed fewer differences between the gut microbiota of R. brelichi and R. roxellana. Correspondingly, no differences were detected in the relative abundances of functional genes between the two Rhinopithecus species. CONCLUSION Taken together, the study highlights that host species have an effect on the composition and function of the gut microbiota of snub-nosed monkeys. Therefore, the host species should be considered when developing nutritional strategies and investigating the effects of niche on the gut microbiota of snub-nosed monkeys.
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Affiliation(s)
- Li Xi
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- Henan Engineering Research Center of Development and Application of Green Feed Additives, Shangqiu Normal University, Shangqiu, China
| | - Xiaohui Wen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | - Jincheng Han
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China.
- Henan Engineering Research Center of Development and Application of Green Feed Additives, Shangqiu Normal University, Shangqiu, China.
| | - Xinxi Qin
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China.
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Yanzhen Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Zihan Wang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
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Amaral WZ, Lubach GR, Rendina DN, Phillips GJ, Lyte M, Coe CL. Significant Microbial Changes Are Evident in the Reproductive Tract of Pregnant Rhesus Monkeys at Mid-Gestation but Their Gut Microbiome Does Not Shift until Late Gestation. Microorganisms 2023; 11:1481. [PMID: 37374982 PMCID: PMC10304935 DOI: 10.3390/microorganisms11061481] [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: 04/10/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Vaginal and rectal specimens were obtained from cycling, pregnant, and nursing rhesus monkeys to assess pregnancy-related changes in the commensal bacteria in their reproductive and intestinal tracts. Using 16S rRNA gene amplicon sequencing, significant differences were found only in the vagina at mid-gestation, not in the hindgut. To verify the apparent stability in gut bacterial composition at mid-gestation, the experiment was repeated with additional monkeys, and similar results were found with both 16S rRNA gene amplicon and metagenomic sequencing. A follow-up study investigated if bacterial changes in the hindgut might occur later in pregnancy. Gravid females were assessed closer to term and compared to nonpregnant females. By late pregnancy, significant differences in bacterial composition, including an increased abundance of 4 species of Lactobacillus and Bifidobacterium adolescentis, were detected, but without a shift in the overall community structure. Progesterone levels were assessed as a possible hormone mediator of bacterial change. The relative abundance of only some taxa (e.g., Bifidobacteriaceae) were specifically associated with progesterone. In summary, pregnancy changes the microbial profiles in monkeys, but the bacterial diversity in their lower reproductive tract is different from women, and the composition of their intestinal symbionts remains stable until late gestation when several Firmicutes become more prominent.
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Affiliation(s)
| | - Gabriele R. Lubach
- Harlow Center for Biological Psychology, University of Wisconsin, Madison, WI 53715, USA; (G.R.L.); (D.N.R.)
| | - Danielle N. Rendina
- Harlow Center for Biological Psychology, University of Wisconsin, Madison, WI 53715, USA; (G.R.L.); (D.N.R.)
- Health and Biosciences, International Flavors & Fragrances (IFF), Wilmington, DE 19803, USA
| | - Gregory J. Phillips
- College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.J.P.); (M.L.)
| | - Mark Lyte
- College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.J.P.); (M.L.)
| | - Christopher L. Coe
- Harlow Center for Biological Psychology, University of Wisconsin, Madison, WI 53715, USA; (G.R.L.); (D.N.R.)
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Zhao G, Qi M, Wang Q, Hu C, Li X, Chen Y, Yang J, Yu H, Chen H, Guo A. Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment. BMC Genomics 2023; 24:62. [PMID: 36737703 PMCID: PMC9896789 DOI: 10.1186/s12864-023-09142-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies. RESULTS The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals. CONCLUSION Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.
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Affiliation(s)
- Gang Zhao
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Qiankun Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Changmin Hu
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xiang Li
- grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jingyuan Yang
- Hubei Key Laboratory of Conservation Biology of Shennongjia Golden Monkey (Shennongjia National Park Administration), Shennongjia Forest Ecosystem Research Station, Shennongjia, 442411 China
| | - Huiliang Yu
- Hubei Key Laboratory of Conservation Biology of Shennongjia Golden Monkey (Shennongjia National Park Administration), Shennongjia Forest Ecosystem Research Station, Shennongjia, 442411 China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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Liu X, Fan Y, Mo T, Chen Q, Chen W. Comparative Study of the Gut Microbiota Community between the Farmed and Wild Mastacembelus armatus (Zig-Zag Eel). Metabolites 2022; 12:metabo12121193. [PMID: 36557231 PMCID: PMC9781078 DOI: 10.3390/metabo12121193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Cultivated and wild fish of the same species may exhibit different characteristics, such as in their flavor, growth and development. In some wild fish species, reproductive functions may even be retarded when wild individuals are moved into cultivated conditions. The gut microbiota may be one of the reasons for these phenomena as they have been reported to play an important role in host growth and development, as well as in normal reproductive functioning. Here, we used Mastacembelus armatus (zig-zag eel), a freshwater fish which shows anormal reproductive function in cultivated conditions, as a model to comparatively study the diversity, structure and function of gut microbiota in cultivated and wild groups by analyzing the 16S rRNA sequence of each group's microbiota. The results showed that Proteobacteria and Firmicutes were the dominant phyla in the gut microbiota of wild (accounting for 45.8% and 20.3% of the total number of Proteobacteria and Firmicutes, respectively) and farmed (accounting for 21.4% and 75.6% of the total number of Proteobacteria and Firmicutes, respectively) zig-zag eel. Wild zig-zag eels (Shannon = 3.56; Chao = 583.08; Ace = 579.18) had significantly higher alpha diversity than those in cultivated populations (Shannon = 2.09; Chao = 85.45; Ace = 86.14). A significant difference in the community structure of the gut microbiota was found between wild and cultivated populations. The wild zig-zag eel showed a high abundance of functional pathways in metabolism, genetic information processing and organismal system function. These results suggested that the diversity and function of gut microbiota in zig-zag eel were correlated with their diet and habitat conditions, which indicated that the management of cultivated populations should mimic the wild diet and habitat to improve the productivity and quality of farmed zig-zag eel.
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9
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Hickmott AJ, Boose KJ, Wakefield ML, Brand CM, Snodgrass JJ, Ting N, White FJ. A comparison of faecal glucocorticoid metabolite concentration and gut microbiota diversity in bonobos ( Pan paniscus). MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35960548 DOI: 10.1099/mic.0.001226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sex, age, diet, stress and social environment have all been shown to influence the gut microbiota. In several mammals, including humans, increased stress is related to decreasing gut microbial diversity and may differentially impact specific taxa. Recent evidence from gorillas shows faecal glucocorticoid metabolite concentration (FGMC) did not significantly explain gut microbial diversity, but it was significantly associated with the abundance of the family Anaerolineaceae. These patterns have yet to be examined in other primates, like bonobos (Pan paniscus). We compared FGMC to 16S rRNA amplicons for 202 bonobo faecal samples collected across 5 months to evaluate the impact of stress, measured with FGMC, on the gut microbiota. Alpha diversity measures (Chao's and Shannon's indexes) were not significantly related to FGMC. FGMC explained 0.80 % of the variation in beta diversity for Jensen-Shannon and 1.2% for weighted UniFrac but was not significant for unweighted UniFrac. We found that genus SHD-231, a member of the family Anaerolinaceae had a significant positive relationship with FGMC. These results suggest that bonobos are relatively similar to gorillas in alpha diversity and family Anaerolinaceae responses to FGMC, but different from gorillas in beta diversity. Members of the family Anaerolinaceae may be differentially affected by FGMC across great apes. FGMC appears to be context dependent and may be species-specific for alpha and beta diversity but this study provides an example of consistent change in two African apes. Thus, the relationship between physiological stress and the gut microbiome may be difficult to predict, even among closely related species.
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Affiliation(s)
- Alexana J Hickmott
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA.,Texas Biomedical Research Institute, San Antonio, TX 78227, USA.,Southwest National Primate Research Center, San Antonio, TX, USA
| | - Klaree J Boose
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Monica L Wakefield
- Sociology, Anthropology, and Philosophy, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA.,Bakar Computational Health Sciences Institute, University of California, San Francisco, USA
| | - J Josh Snodgrass
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Frances J White
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
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10
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Asangba AE, Mugisha L, Rukundo J, Lewis RJ, Halajian A, Cortés-Ortiz L, Junge RE, Irwin MT, Karlson J, Perkin A, Watsa M, Erkenswick G, Bales KL, Patton DL, Jasinska AJ, Fernandez-Duque E, Leigh SR, Stumpf RM. Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates. Microbiol Spectr 2022; 10:e0164321. [PMID: 35587638 PMCID: PMC9241786 DOI: 10.1128/spectrum.01643-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 04/28/2022] [Indexed: 11/20/2022] Open
Abstract
The study of the mammalian microbiome serves as a critical tool for understanding host-microbial diversity and coevolution and the impact of bacterial communities on host health. While studies of specific microbial systems (e.g., in the human gut) have rapidly increased, large knowledge gaps remain, hindering our understanding of the determinants and levels of variation in microbiomes across multiple body sites and host species. Here, we compare microbiome community compositions from eight distinct body sites among 17 phylogenetically diverse species of nonhuman primates (NHPs), representing the largest comparative study of microbial diversity across primate host species and body sites. Analysis of 898 samples predominantly acquired in the wild demonstrated that oral microbiomes were unique in their clustering, with distinctive divergence from all other body site microbiomes. In contrast, all other body site microbiomes clustered principally by host species and differentiated by body site within host species. These results highlight two key findings: (i) the oral microbiome is unique compared to all other body site microbiomes and conserved among diverse nonhuman primates, despite their considerable dietary and phylogenetic differences, and (ii) assessments of the determinants of host-microbial diversity are relative to the level of the comparison (i.e., intra-/inter-body site, -host species, and -individual), emphasizing the need for broader comparative microbial analyses across diverse hosts to further elucidate host-microbial dynamics, evolutionary and biological patterns of variation, and implications for human-microbial coevolution. IMPORTANCE The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution.
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Affiliation(s)
- Abigail E. Asangba
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lawrence Mugisha
- Ecohealth Research Group, Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda
- Department of Wildlife & Aquatic Animal Resources, College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Joshua Rukundo
- Chimpanzee Sanctuary and Wildlife Conservation (Chimpanzee Trust), Ngamba Island, Uganda
| | - Rebecca J. Lewis
- Department of Anthropology, University of Texas at Austin, Austin, Texas, USA
| | - Ali Halajian
- Research Administration and Development, University of Limpopo, Sovenga, South Africa
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Mitchell T. Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, Illinois, USA
| | - Johan Karlson
- Tanzania Forest Conservation Group and Nocturnal Primate Research Group, Dar es Salaam, Tanzania
| | - Andrew Perkin
- Tanzania Forest Conservation Group and Nocturnal Primate Research Group, Dar es Salaam, Tanzania
| | - Mrinalini Watsa
- San Diego Zoo Wildlife Alliance, San Diego, California, USA
- Field Projects International, Escondido, California, USA
| | - Gideon Erkenswick
- Field Projects International, Escondido, California, USA
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Karen L. Bales
- Department of Psychology, University of California Davis, Davis, California, USA
| | - Dorothy L. Patton
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Anna J. Jasinska
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | - Steven R. Leigh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Anthropology, University of Colorado—Boulder, Boulder, Colorado, USA
| | - Rebecca M. Stumpf
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Kanyanchu River Chimpanzee Project and Research Collaborative, Bigodi, Uganda
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Notre Dame Institute for Advanced Study, University of Notre Dame, Notre Dame, Indiana, USA
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11
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Tang S, Li Y, Huang C, Yan S, Li Y, Chen Z, Wu Z. Comparison of Gut Microbiota Diversity Between Captive and Wild Tokay Gecko (Gekko gecko). Front Microbiol 2022; 13:897923. [PMID: 35783386 PMCID: PMC9248866 DOI: 10.3389/fmicb.2022.897923] [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: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
Captive animals and wild animals may exhibit different characteristics due to the heterogeneity of their living environments. The gut microbiota play an important role in the digestion and absorption, energy metabolism, immune regulation, and physiological health of the host. However, information about the gut microbiota of captive and wild Gekko gecko is currently limited. To determine the difference in gut microbiota community composition, diversity, and structure between captive and wild geckos, we used the Illumina miseq platform to conduct high-throughput sequencing and bioinformatics analysis of the v3–v4 hypervariable region of 16S rRNA in 54 gecko samples. Our results showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant gut microbiota phyla of the gecko. The dominant genera comprised mainly Pseudomonas, Burkholderia-caballeronia-paraburkholderia, Ralstonia, Romboutsia, and Bacteroides. Captive geckos had significantly higher alpha diversity and potential pathogenic bacteria than wild populations. Moreover, significant differences in beta diversity of gut microbiota were observed between two populations. Functional prediction analysis showed that the relative abundance of functional pathways of wild geckos was more higher in metabolism, genetic information processing and organismal system function than those in captive geckos. Total length significantly affected gut microbial community (R2 = 0.4527, p = 0.001) and explained 10.45% of the total variation for gut microbial community variance between two groups. These results may be related to differences in diet and living environment between two populations, suggesting that the management of captive populations should mimic wild environments to the greatest extent possible to reduce the impact on their gut microbiota.
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Affiliation(s)
- Sanqi Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Chengming Huang
- Key Laboratory of Animal Ecology and Conservation, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shufa Yan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Yongtai Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Zening Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- Zening Chen,
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- *Correspondence: Zhengjun Wu,
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12
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Bloomfield LSP, Tracey C, Mbabazi E, Schultz RL, Henderson R, Bardosh K, Randolph S, Paige S. Research Participation Influences Willingness to Reduce Zoonotic Exposure in Uganda. ECOHEALTH 2022; 19:299-314. [PMID: 35674864 DOI: 10.1007/s10393-022-01589-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
The majority of emerging and re-emerging infectious diseases in people are zoonotic. Despite substantial research in communities adjacent to protected areas with high levels of biodiversity, limited data exist on people's knowledge, attitudes, and practices to avoid exposure to infections from domestic and wild animals. We used a modified grounded-theory framework in QS NVivo to develop a Knowledge, Attitude, and Practices (KAP) survey administered at two time points, KAPT1 (April-July 2016) and KAPT2 (February-May 2018) to participants living at the edge of Kibale National Park, Uganda. We measured the difference in willingness to engage in protective behaviors around zoonotic exposure between an Intervention group (n = 61) and a Comparison group (n = 125). Prior to KAPT1, the Intervention group engaged in a human-centered design (HCD) activity identifying behaviors that reduce zoonotic exposure (March-May 2016). Using a difference-in-difference approach, we compared the Intervention and Comparison groups to assess sustained willingness and use of protective behaviors against domestic and wild animal exposures. At KAPT1, Comparison group participants had a significantly lower (p < 0.05) level of willingness to engage in behaviors that increase exposure to zoonoses from domestic animals; Intervention group participants had a significantly higher (p < 0.01) level of willingness to engage in behaviors that increase exposure to zoonoses from wild animals. At KAPT2, the treatment effect was significant (p < 0.01) for sustained willingness to engage in protective behaviors for domestic animal exposure in the Intervention group. There were no significant differences in practices to avoid domestic and wild animal zoonotic exposure between the Intervention and Comparison groups.
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Affiliation(s)
- Laura S P Bloomfield
- Stanford University School of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Emmett Interdisciplinary Program in Environment and Resources, Stanford University, Stanford, CA, 94305, USA.
| | - Christopher Tracey
- Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Edith Mbabazi
- Makerere University Biological Field Station, Kibale National Park, Kibale, Uganda
| | - Rhiannon L Schultz
- Department of Anthropology, University of Georgia, Athens, GA, 30602, USA
| | - Rebecca Henderson
- Department of Anthropology, University of Florida, Gainesville, FL, 32607, USA
| | - Kevin Bardosh
- Center for One Health Research, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Shannon Randolph
- School of Humanities and Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Sarah Paige
- Global Health Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
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13
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McManus N, Holmes SM, Louis EE, Johnson SE, Baden AL, Amato KR. The gut microbiome as an indicator of habitat disturbance in a Critically Endangered lemur. BMC Ecol Evol 2021; 21:222. [PMID: 34915861 PMCID: PMC8680155 DOI: 10.1186/s12862-021-01945-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Habitat disturbance affects the biology and health of animals globally. Understanding the factors that contribute to the differential responses of animals to habitat disturbance is critical for conservation. The gut microbiota represents a potential pathway through which host responses to habitat disturbance might be mediated. However, a lack of quantitative environmental data in many gut microbiome (GM) studies of wild animals limits our ability to pinpoint mechanisms through which habitat disturbance affects the GM. Here, we examine the impact of anthropogenic habitat disturbance on the diet and GM of the Critically Endangered black-and-white ruffed lemur (Varecia variegata editorum). We collected fecal samples and behavioral data from Varecia occupying habitats qualitatively categorized as primary forest, moderately disturbed forest, and heavily disturbed forest. RESULTS Varecia diet and GM composition differed substantially across sites. Dietary richness predicted GM richness across sites, and overall GM composition was strongly correlated to diet composition. Additionally, the consumption of three specific food items positively correlated to the relative abundances of five microbial strains and one microbial genus across sites. However, diet did not explain all of the GM variation in our dataset, and differences in the GM were detected that were not correlated with diet, as measured. CONCLUSIONS Our data suggest that diet is an important influence on the Varecia GM across habitats and thus could be leveraged in novel conservation efforts in the future. However, other factors such as contact with humans should also be accounted for. Overall, we demonstrate that quantitative data describing host habitats must be paired with GM data to better target the specific mechanisms through which environmental change affects the GM.
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Affiliation(s)
- Nicolette McManus
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Sheila M Holmes
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo, Omaha, NE, 68107, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York, NY, 10065, USA.
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA.
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14
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Ingala MR, Simmons NB, Dunbar M, Wultsch C, Krampis K, Perkins SL. You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches. Anim Microbiome 2021; 3:82. [PMID: 34906258 PMCID: PMC8672517 DOI: 10.1186/s42523-021-00139-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/20/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts and their gut bacteria, fewer studies examine the potentially adaptive functional contributions of these microbes to the dietary habits of their hosts. In this study, we examined predicted metabolic pathways in the gut bacteria of more than 500 individual bats belonging to 60 species and compare the enrichment of these functions across hosts with distinct dietary ecologies. RESULTS We found that predicted microbiome functions were differentially enriched across hosts with different diets. Using a machine-learning approach, we also found that inferred microbiome functions could be used to predict specialized host diets with reasonable accuracy. We detected a relationship between both host phylogeny and diet with respect to microbiome functional repertoires. Because many predicted functions could potentially fill nutritional gaps for bats with specialized diets, we considered pathways discriminating dietary niches as traits of the host and fit them to comparative phylogenetic models of evolution. Our results suggest that some, but not all, predicted microbiome functions may evolve toward adaptive optima and thus be visible to the forces of natural selection operating on hosts over evolutionary time. CONCLUSIONS Our results suggest that bats with specialized diets may partially rely on their gut microbes to fulfill or augment critical nutritional pathways, including essential amino acid synthesis, fatty acid biosynthesis, and the generation of cofactors and vitamins essential for proper nutrition. Our work adds to a growing body of literature suggesting that animal microbiomes are structured by a combination of ecological and evolutionary processes and sets the stage for future metagenomic and metabolic characterization of the bat microbiome to explore links between bacterial metabolism and host nutrition.
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Affiliation(s)
- Melissa R. Ingala
- Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC USA
- Department of Mammalogy, The American Museum of Natural History, New York, NY USA
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY USA
| | - Nancy B. Simmons
- Department of Mammalogy, The American Museum of Natural History, New York, NY USA
| | - Miranda Dunbar
- Department of Biological Sciences, Southern Connecticut State University, New Haven, CT USA
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, The American Museum of Natural History, New York, NY USA
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY USA
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY USA
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY USA
| | - Susan L. Perkins
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY USA
- Sackler Institute for Comparative Genomics, The American Museum of Natural History, New York, NY USA
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15
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Grassotti TT, Kothe CI, Prichula J, Mohellibi N, Mann MB, Wagner PGC, Campos FS, Campos AAS, Frazzon J, Frazzon APG. Fecal bacterial communities of wild black capuchin monkeys ( Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100048. [PMID: 34841339 PMCID: PMC8610302 DOI: 10.1016/j.crmicr.2021.100048] [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: 03/09/2021] [Revised: 06/19/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria ( χ ¯ = 80.54%), followed by Firmicutes ( χ ¯ = 12.14%), Actinobacteria ( χ ¯ = 4.60%), and Bacteriodetes ( χ ¯ = 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates.
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Key Words
- FROGS, Find Rapidly OTUs with Galaxy Solution
- FastQC, Fast Quality Control
- Fecal microbiota
- HTS, high-throughput sequencing
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MultiQC, Multi Quality Control
- OTUs, Operational Taxonomic Units
- PGMTM, Personal Genome Machine
- PICRUSt2, Phylogenetic Investigation of Communities by Reconstruction of Unobserved State
- Primate conservation
- Proteobacteria
- Robust capuchins
- SCS, Santa Cruz do Sul
- SSC, São Sebastião do Caí
- SSU, Small Subunit rRNA gene
- Wild south Brazilian primates
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Affiliation(s)
- Tiela Trapp Grassotti
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Janira Prichula
- Department of Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, RS, Brazil
| | - Nacer Mohellibi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Michele Bertoni Mann
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Fabricio Souza Campos
- Laboratory of Bioinformatics and Biotechnology, Campus de Gurupi, Federal University of Tocantins, Gurupi, TO, Brazil; Federal University of Tocantins, Federal University of Tocantins, Palmas, TO, Brazil
| | | | - Jeverson Frazzon
- Biochemistry and Molecular Biology of Microorganisms Laboratory, Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Paula Guedes Frazzon
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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16
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Mehl C, Schoeman MC, Sanko TJ, Bezuidenhout C, Mienie CMS, Preiser W, Vosloo D. Wastewater treatment works change the intestinal microbiomes of insectivorous bats. PLoS One 2021; 16:e0247475. [PMID: 33657147 PMCID: PMC7928523 DOI: 10.1371/journal.pone.0247475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022] Open
Abstract
Mammals, born with a near-sterile intestinal tract, are inoculated with their mothers’ microbiome during birth. Thereafter, extrinsic and intrinsic factors shape their intestinal microbe assemblage. Wastewater treatment works (WWTW), sites synonymous with pollutants and pathogens, receive influent from domestic, agricultural and industrial sources. The high nutrient content of wastewater supports abundant populations of chironomid midges (Diptera), which transfer these toxicants and potential pathogens to their predators, such as the banana bat Neoromicia nana (Vespertilionidae), thereby influencing their intestinal microbial assemblages. We used next generation sequencing and 16S rRNA gene profiling to identify and compare intestinal bacteria of N. nana at two reference sites and two WWTW sites. We describe the shared intestinal microbiome of the insectivorous bat, N. nana, consisting of seven phyla and eleven classes. Further, multivariate analyses revealed that location was the most significant driver (sex, body size and condition were not significant) of intestinal microbiome diversity. Bats at WWTW sites exhibited greater intestinal microbiota diversity than those at reference sites, likely due to wastewater exposure, stress and/or altered diet. Changes in their intestinal microbiota assemblages may allow these bats to cope with concomitant stressors.
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Affiliation(s)
- Calvin Mehl
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - M. Corrie Schoeman
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tomasz J. Sanko
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Carlos Bezuidenhout
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Charlotte M. S. Mienie
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg Hospital, Tygerberg, South Africa
| | - Dalene Vosloo
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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17
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Kuthyar S, Kowalewski MM, Roellig DM, Mallott EK, Zeng Y, Gillespie TR, Amato KR. Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria. Ecol Evol 2021; 11:45-57. [PMID: 33437414 PMCID: PMC7790644 DOI: 10.1002/ece3.6910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/27/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.
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Affiliation(s)
- Sahana Kuthyar
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
| | - Martin M. Kowalewski
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
- Estación Biológica CorrientesMuseo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN‐CONICET)CorrientesArgentina
| | - Dawn M. Roellig
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention (CDC)AtlantaGAUSA
| | | | - Yan Zeng
- Department of AnthropologyNorthwestern UniversityEvanstonILUSA
| | - Thomas R. Gillespie
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Ecology, and Evolutionary BiologyEmory UniversityAtlantaGAUSA
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18
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Stothart MR, Greuel RJ, Gavriliuc S, Henry A, Wilson AJ, McLoughlin PD, Poissant J. Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters. Mol Ecol 2020; 30:555-571. [PMID: 33231332 DOI: 10.1111/mec.15747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022]
Abstract
Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.
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Affiliation(s)
- Mason R Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Stefan Gavriliuc
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Astrid Henry
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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19
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Narat V, Amato KR, Ranger N, Salmona M, Mercier-Delarue S, Rupp S, Ambata P, Njouom R, Simon F, Giles-Vernick T, LeGoff J. A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo. Sci Rep 2020; 10:19107. [PMID: 33154444 PMCID: PMC7645722 DOI: 10.1038/s41598-020-75847-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, UMR7206 CNRS/MNHN/Université de Paris, Site du Musée de L'Homme, Paris, France
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, USA
- Humans and the Microbiome, CIFAR, Toronto, Canada
| | - Noémie Ranger
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Maud Salmona
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France
| | | | - Stephanie Rupp
- Department of Anthropology, City University of New York - Lehman College, New York, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Tamara Giles-Vernick
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France.
- Humans and the Microbiome, CIFAR, Toronto, Canada.
| | - Jérôme LeGoff
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France.
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France.
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20
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de Winter II, Umanets A, Gort G, Nieuwland WH, van Hooft P, Heitkönig IMA, Kappeler PM, Prins HHT, Smidt H. Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs. Sci Rep 2020; 10:16818. [PMID: 33033341 PMCID: PMC7544911 DOI: 10.1038/s41598-020-73827-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Gastrointestinal helminth-microbiota associations are shaped by various ecological processes. The effect of the ecological context of the host on the bacterial microbiome and gastrointestinal helminth parasites has been tested in a number of ecosystems and experimentally. This study takes the important step to look at these two groups at the same time and to start to examine how these communities interact in a changing host environment. Fresh faecal samples (N = 335) from eight wild Eulemur populations were collected over 2 years across Madagascar. We used 16S ribosomal RNA gene sequencing to characterise the bacterial microbiota composition, and faecal flotation to isolate and morphologically identify nematode eggs. Infections with nematodes of the genera Callistoura and Lemuricola occurred in all lemur populations. Seasonality significantly contributed to the observed variation in microbiota composition, especially in the dry deciduous forest. Microbial richness and Lemuricola spp. infection prevalence were highest in a previously intensely logged site, whereas Callistoura spp. showed no such pattern. In addition, we observed significant correlations between gastrointestinal parasites and bacterial microbiota composition in these lemurs, with 0.4-0.7% of the variation in faecal bacterial microbiota composition being explained by helminth infections. With this study, we show effects of environmental conditions on gastrointestinal nematodes and bacterial interactions in wild lemurs and believe it is essential to consider the potential role of microbiome-parasite associations on the hosts' GI stability, health, and survival.
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Affiliation(s)
- I I de Winter
- Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, The Netherlands.
| | - A Umanets
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - G Gort
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - W H Nieuwland
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, The Netherlands
| | - P van Hooft
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, The Netherlands
| | - I M A Heitkönig
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, The Netherlands
| | - P M Kappeler
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - H H T Prins
- Animal Sciences Group, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - H Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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21
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Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190598. [PMID: 32772669 PMCID: PMC7435160 DOI: 10.1098/rstb.2019.0598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2020] [Indexed: 12/23/2022] Open
Abstract
Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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22
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Scheelings TF, Moore RJ, Van TTH, Klaassen M, Reina RD. The gut bacterial microbiota of sea turtles differs between geographically distinct populations. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The microbiota of metazoans can be influenced by a variety of factors including diet, environment and genetics. In this study we sampled multiple populations from 2 host species that do not overlap in distribution, in order to test whether their bacterial microbiotas are species-specific or more variable. Intestinal swabs were collected from loggerhead turtles originating from Florida, USA, and Queensland, Australia, as well as from flatback turtles from Crab Island, Queensland, and Port Hedland, Western Australia. We then manually extracted bacterial DNA and used 16S rRNA sequencing to explore bacterial microbial community composition and structure. Our investigation showed that the bacterial microbiota of sea turtles is heavily influenced by geography, with loggerhead turtles originating from the USA and Australia harbouring significantly different bacterial microbial populations in terms of composition. Similarly, we also found that flatback turtles from Crab Island had significantly less diverse microbiotas, with a predominance of the bacterial phylum Firmicutes, in comparison to their genetically similar counterparts from Port Hedland. Factors that may explain these observed differences between populations include host genetics, differences in foraging habitat quality and differences in migratory distance (and thus durations of inappetence) between foraging and breeding grounds. The mechanisms by which these factors may influence bacterial microbial composition of sea turtle gastrointestinal tracts warrants further investigation. The results of this study highlight the importance of interpreting microbiota data of wild animals in the context of geography.
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Affiliation(s)
- TF Scheelings
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria 3800, Australia
| | - RJ Moore
- School of Science, RMIT University, Bundoora West Campus, Plenty Rd, Bundoora, Victoria 3083, Australia
| | - TTH Van
- School of Science, RMIT University, Bundoora West Campus, Plenty Rd, Bundoora, Victoria 3083, Australia
| | - M Klaassen
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - RD Reina
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria 3800, Australia
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23
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Antimicrobial Peptide GH12 Prevents Dental Caries by Regulating Dental Plaque Microbiota. Appl Environ Microbiol 2020; 86:AEM.00527-20. [PMID: 32414800 DOI: 10.1128/aem.00527-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/11/2020] [Indexed: 02/05/2023] Open
Abstract
Due to the complex microecology and microenvironment of dental plaque, novel caries prevention strategies require modulating the microbial communities ecologically and reducing the cariogenic properties effectively. Antimicrobial peptide GH12 reduced the lactic acid production and exopolysaccharide (EPS) synthesis of a Streptococcus mutans biofilm and a three-species biofilm in vitro in previous studies. However, the anticaries effects and microecological effects of GH12 remained to be investigated in a complex biofilm model in vitro and an animal caries model in vivo In the present study, GH12 at 64 mg/liter showed the most effective inhibition of lactic acid production, EPS synthesis, pH decline, and biofilm integrity of human dental plaque-derived multispecies biofilms in vitro, and GH12 at 64 mg/liter was therefore chosen for use in subsequent in vitro and in vivo assays. When treated with 64-mg/liter GH12, the dental plaque-derived multispecies biofilms sampled from healthy volunteers maintained its microbial diversity and showed a microbial community structure similar to that of the control group. In the rat caries model with a caries-promoting diet, 64-mg/liter GH12 regulated the microbiota of dental plaque, in which the abundance of caries-associated bacteria was decreased and the abundance of commensal bacteria was increased. In addition, 64-mg/liter GH12 significantly reduced the caries scores of sulcal and smooth surface caries in all locations. In conclusion, GH12 inhibited the cariogenic properties of dental plaque without perturbing the dental plaque microbiota of healthy individuals and GH12 regulated the dysbiotic microbial ecology and arrested caries development under cariogenic conditions.IMPORTANCE The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo This study thus describes an alternative antimicrobial therapy for dental caries.
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24
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The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance. mSystems 2020; 5:5/3/e00061-20. [PMID: 32457237 PMCID: PMC7253362 DOI: 10.1128/msystems.00061-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications. Human exploitation and destruction of tropical resources are currently threatening innumerable wild animal species, altering natural ecosystems and thus, food resources, with profound effects on gut microbiota. Given their conservation status and the importance to tropical ecosystems, wild nonhuman primates make excellent models to investigate the effect of human disturbance on the diversity of host-associated microbiota. Previous investigations have revealed a loss of fecal bacterial diversity in primates living in degraded compared to intact forests. However, these data are available for a limited number of species, and very limited information is available on the fungal taxa hosted by the gut. Here, we estimated the diversity and composition of gut bacterial and fungal communities in two primates living sympatrically in both human-modified and pristine forests in the Udzungwa Mountains of Tanzania. Noninvasively collected fecal samples of 12 groups of the Udzungwa red colobus (Procolobus gordonorum) (n = 89), a native and endangered primate (arboreal and predominantly leaf-eating), and five groups of the yellow baboon (Papio cynocephalus) (n = 69), a common species of least concern (ground-feeding and omnivorous), were analyzed by the V1-V3 region of the 16S rRNA gene (bacterial) and ITS1-ITS2 (fungal) sequencing. Gut bacterial diversities were associated with habitat in both species, most likely depending on their ecological niches and associated digestive physiology, dietary strategies, and locomotor behavior. In addition, fungal communities also show distinctive traits across hosts and habitat type, highlighting the importance of investigating this relatively unexplored gut component. IMPORTANCE Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.
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25
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Ni Q, He X, Zeng B, Meng X, Xu H, Li Y, Yang M, Li D, Yao Y, Zhang M, Li Y, Fan X, Yang D, Xie M. Variation in Gut Microbiota of Captive Bengal Slow Lorises. Curr Microbiol 2020; 77:2623-2632. [PMID: 32440808 DOI: 10.1007/s00284-020-02035-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
Abstract
Gastrointestinal microbiome plays an important role in animal metabolism, immune system and pathology associated with health and disease. Many wild slow lorises were confiscated from illegal trade into captivities and experienced a range of changes in living environment and diet. Microbiome analysis contributes to improving captive management by identifying the alteration in their gastrointestinal microbial communities and aiding in determining the factors affecting the health of captive slow lorises. The fecal samples of eighteen Bengal slow lorises (Nycticebus bengalensis) were used to compare gut microbiota from four rescue centers located in Dehong, Gejiu, Nanning and Puer cities of China. The results showed a significant site-dependent difference in microbial community diversity. Similar to other Lorisinae species, the Phyla including Bacteroidetes, Firmicutes and Proteobacteria dominated their gut microbiome composition. The Gejiu group exhibited a higher overall diversity and the unique OTUs, which is resulted from long-term isolated husbandry and heavy human disturbances. The scarcity of gums in the captive diet was likely to cause a lower abundance of Prevotella associated with soluble fiber degradation. The variation of intestinal microbiota in different environments highlights the necessity to improve feed preparation and husbandry management for the captive Bengal slow lorises.
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Affiliation(s)
- Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China. .,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
| | - Xin He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiangyun Meng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.,College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, 46 Xinkang Road, Yaan, 625014, China.
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26
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Huan Z, Yao Y, Yu J, Chen H, Li M, Yang C, Zhao B, Ni Q, Zhang M, Xie M, Xu H. Differences in the gut microbiota between Cercopithecinae and Colobinae in captivity. J Microbiol 2020; 58:367-376. [PMID: 32266563 DOI: 10.1007/s12275-020-9493-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/16/2022]
Abstract
The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.
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Affiliation(s)
- Zongjin Huan
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, P. R. China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, P. R. China.,Chengdu Zoo (Chengdu Wildlife Research Institute), Chengdu, 610081, P. R. China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, P. R. China
| | - Jianqiu Yu
- Chengdu Zoo (Chengdu Wildlife Research Institute), Chengdu, 610081, P. R. China
| | - Hongwei Chen
- Chengdu Zoo (Chengdu Wildlife Research Institute), Chengdu, 610081, P. R. China
| | - Meirong Li
- Nanjing Hongshan Forest Zoo, Nanjing, P. R. China
| | - Chaojun Yang
- Giant Panda National Park Authority, Sichuan, P. R. China
| | - Bo Zhao
- Chengdu Zoo (Chengdu Wildlife Research Institute), Chengdu, 610081, P. R. China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, P. R. China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, P. R. China.
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27
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Grieneisen LE, Charpentier MJE, Alberts SC, Blekhman R, Bradburd G, Tung J, Archie EA. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc Biol Sci 2020; 286:20190431. [PMID: 31014219 DOI: 10.1098/rspb.2019.0431] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population FST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.
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Affiliation(s)
- Laura E Grieneisen
- 1 Department of Genetics, Cell Biology, and Development, University of Minnesota , Minneapolis, MN 55455 , USA.,2 Department of Biology, University of Notre Dame , Notre Dame, IN 46556 , USA
| | - Marie J E Charpentier
- 3 Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE , Montpellier , France
| | - Susan C Alberts
- 4 Department of Biology, Duke University , Durham, NC 27708 , USA.,5 Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
| | - Ran Blekhman
- 1 Department of Genetics, Cell Biology, and Development, University of Minnesota , Minneapolis, MN 55455 , USA.,7 Department of Ecology, Evolution, and Behavior, University of Minnesota , Minneapolis, MN 55455 , USA
| | - Gideon Bradburd
- 8 Department of Integrative Biology, Michigan State University , East Lansing, MI 48824 , USA
| | - Jenny Tung
- 4 Department of Biology, Duke University , Durham, NC 27708 , USA.,5 Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
| | - Elizabeth A Archie
- 2 Department of Biology, University of Notre Dame , Notre Dame, IN 46556 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
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28
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Hanya G. Gut microbiota composition of Japanese macaques associates with extent of human encroachment. Am J Primatol 2019; 81:e23072. [PMID: 31788810 DOI: 10.1002/ajp.23072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/29/2019] [Accepted: 11/10/2019] [Indexed: 12/28/2022]
Abstract
In recent decades, human-wildlife interaction and associated anthropogenic food provisioning has been increasing and becoming more severe due to fast population growth and urban development. Noting the role of the gut microbiome in host physiology like nutrition and health, it is thus essential to understand how human-wildlife interactions and availability of anthropogenic food in habitats can affect an animal's gut microbiome. This study, therefore, set out to examine the gut microbiota of Japanese macaques (Macaca fuscata) with varying accessibility to anthropogenic food and the possibility of using gut microbiota as indicator for macaques' reliance on anthropogenic food. Using 16S ribosomal RNA gene sequencing, we described the microbial composition of Japanese macaques experiencing different types of human disturbance and anthropogenic food availability-captive, provisioned, crop-raiding, and wild. In terms of alpha diversity, our results showed that observed richness of gut microbiota did not differ significantly between disturbance types but among collection sites, whereas Shannon diversity index differed by both disturbance types and sites. In terms of beta diversity, captive populations harbored the most distinctive gut microbial composition, and had the greatest difference compared with wild populations. Whereas for provisioned and crop-raiding groups, the macaques exhibited intermediate microbiota between wild and captive. We identified several potential bacterial taxa at different taxonomic ranks whose abundance potentially could help in assessing macaques' accessibility to anthropogenic food. This study revealed the flexibility of the gut microbiome of Japanese macaques and provided possible indices based on the gut microbiome profile in assessing macaques' accessibility to/reliance on anthropogenic foods.
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Affiliation(s)
- Wanyi Lee
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Japan Monkey Centre, Inuyama, Aichi, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Goro Hanya
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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29
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Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol 2019; 81:e22970. [PMID: 30941803 PMCID: PMC7193701 DOI: 10.1002/ajp.22970] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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30
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Koo BS, Hwang EH, Kim G, Oh H, Son Y, Lee D, Lim KS, Kang P, Lee S, Lee HY, Jeong KJ, Lee Y, Baek SH, Jeon CY, Park SJ, Kim YH, Huh JW, Jin YB, Kim SU, Lee SR, Hong JJ. Evaluation of fecal microbiomes associated with obesity in captive cynomolgus monkeys ( Macaca fascicularis). J Vet Sci 2019; 20:e19. [PMID: 31161737 PMCID: PMC6538515 DOI: 10.4142/jvs.2019.20.e19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 01/02/2023] Open
Abstract
Microorganisms play important roles in obesity; however, the role of the gut microbiomes in obesity is controversial because of the inconsistent findings. This study investigated the gut microbiome communities in obese and lean groups of captive healthy cynomolgus monkeys reared under strict identical environmental conditions, including their diet. No significant differences in the relative abundance of Firmicutes, Bacteroidetes and Prevotella were observed between the obese and lean groups, but a significant difference in Spirochetes (p < 0.05) was noted. Microbial diversity and richness were similar, but highly variable results in microbial composition, diversity, and richness were observed in individuals, irrespective of their state of obesity. Distinct clustering between the groups was not observed by principal coordinate analysis using an unweighted pair group method. Higher sharedness values (95.81% ± 2.28% at the genus level, and 79.54% ± 5.88% at the species level) were identified among individual monkeys. This paper reports the association between the gut microbiome and obesity in captive non-human primate models reared under controlled environments. The relative proportion of Firmicutes and Bacteroidetes as well as the microbial diversity known to affect obesity were similar in the obese and lean groups of monkeys reared under identical conditions. Therefore, obesity-associated microbial changes reported previously appear to be associated directly with environmental factors, particularly diet, rather than obesity.
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Affiliation(s)
- Bon Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Eun Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Hanseul Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Yeonghoon Son
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Dongho Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Kyung Seob Lim
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Philyong Kang
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sangil Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Hwal Yong Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Kang Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Seung Ho Baek
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Chang Yeop Jeon
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sang Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Young Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Jae Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sun Uk Kim
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sang Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea.
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31
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Firrman J, Liu L, Tanes C, Bittinger K, Mahalak K, Rinaldi W. Metagenomic assessment of the Cebus apella gut microbiota. Am J Primatol 2019; 81:e23023. [PMID: 31240754 DOI: 10.1002/ajp.23023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 05/13/2019] [Accepted: 05/27/2019] [Indexed: 12/19/2022]
Abstract
Cebus Apella (C. apella) is a species of Nonhuman Primate (NHP) used for biomedical research because it is phylogenetically similar and shares anatomical commonalities with humans. Here, the gut microbiota of three C. apella were examined in the different regions of the intestinal tract. Using metagenomics, the gut microbiota associated with the luminal content and mucus layer for each intestinal region was identified, and functionality was investigated by quantifying the levels of short chain fatty acids (SCFAs) produced. The results of this study show a high degree of similarity in the intestinal communities among C. apella subjects, with multiple shared characteristics. First, the communities in the lumen were more phylogenetically diverse and rich compared to the mucus layer communities throughout the entire intestinal tract. The small intestine communities in the lumen displayed a higher Shannon diversity index compared to the colon communities. Second, all the communities were dominated by aero-tolerant taxa such as Streptococcus, Enterococcus, Abiotrophia, and Lactobacillus, although there was preferential colonization of specific taxa observed. Finally, the primary SCFA produced throughout the intestinal tract was acetic acid, with some propionic acid and butyric acid detected in the colon regions. The small intestine microbiota produced significantly less SCFAs compared to the communities in the colon. Collectively, these data provide an in-depth report on the composition, distribution, and SCFA production of the gut microbiota along the intestinal tract of the C. apella NHP animal model.
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Affiliation(s)
- Jenni Firrman
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, Pennsylvania
| | - LinShu Liu
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, Pennsylvania
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Karley Mahalak
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, Pennsylvania
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32
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Ingala MR, Becker DJ, Bak Holm J, Kristiansen K, Simmons NB. Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats. Ecol Evol 2019; 9:6508-6523. [PMID: 31236240 PMCID: PMC6580296 DOI: 10.1002/ece3.5228] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/28/2022] Open
Abstract
Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land-use change on wildlife microbiotas, we analyzed long-term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross-species pathogen transmission.
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Affiliation(s)
- Melissa R. Ingala
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNew York
- Division of Vertebrate Zoology, Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew York
| | - Daniel J. Becker
- Odum School of EcologyUniversity of GeorgiaAthensGeorgia
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGeorgia
- Department of BiologyIndiana UniversityBloomingtonIndiana
| | - Jacob Bak Holm
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Clinical‐MicrobiomicsCopenhagenDenmark
| | - Karsten Kristiansen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- BGIShenzhenChina
| | - Nancy B. Simmons
- Division of Vertebrate Zoology, Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew York
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33
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Simons ND, Eick GN, Ruiz-Lopez MJ, Hyeroba D, Omeja PA, Weny G, Zheng H, Shankar A, Frost SDW, Jones JH, Chapman CA, Switzer WM, Goldberg TL, Sterner KN, Ting N. Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection. Genome Biol Evol 2019; 11:1630-1643. [PMID: 31106820 PMCID: PMC6561381 DOI: 10.1093/gbe/evz099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to human immunodeficiency virus in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.
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Affiliation(s)
| | - Geeta N Eick
- Department of Anthropology, University of Oregon
| | | | - David Hyeroba
- College of Veterinary Medicine, Animal Resources, and Bio-Security, Makerere University, Kampala, Uganda
| | - Patrick A Omeja
- Makerere University Biological Field Station, Fort Portal, Uganda
| | - Geoffrey Weny
- Makerere University Biological Field Station, Fort Portal, Uganda
| | - HaoQiang Zheng
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - James H Jones
- Department of Earth System Science, Woods Institute for the Environment, Stanford University
| | - Colin A Chapman
- Makerere University Biological Field Station, Fort Portal, Uganda
- Department of Anthropology, McGill School of Environment, McGill University, Montreal, Quebec, Canada
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison
- Global Health Institute, University of Wisconsin-Madison
| | | | - Nelson Ting
- Department of Anthropology, University of Oregon
- Institute of Ecology and Evolution, University of Oregon
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34
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Nagpal R, Shively CA, Register TC, Craft S, Yadav H. Gut microbiome-Mediterranean diet interactions in improving host health. F1000Res 2019; 8:699. [PMID: 32704349 PMCID: PMC7359750 DOI: 10.12688/f1000research.18992.1] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2019] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota plays a fundamental role in host health and disease. Host diet is one of the most significant modulators of the gut microbial community and its metabolic activities. Evidence demonstrates that dietary patterns such as the 'Western diet' and perturbations in gut microbiome (dysbiosis) have strong associations with a wide range of human diseases, including obesity, metabolic syndrome, type-2 diabetes and cardiovascular diseases. However, consumption of Mediterranean-style diets is considered healthy and associated with the prevention of cardiovascular and metabolic diseases, colorectal cancers and many other diseases. Such beneficial effects of the Mediterranean diet might be attributed to high proportion of fibers, mono- and poly-unsaturated fatty acids, antioxidants and polyphenols. Concurrent literature has demonstrated beneficial modulation of the gut microbiome following a Mediterranean-style diet in humans as well as in experimental animal models such as rodents. We recently demonstrated similar positive changes in the gut microbiome of non-human primates consuming a Mediterranean-style diet for long term (30 months). Therefore, it is rational to speculate that this positive modulation of the gut microbiome diversity, composition and function is one of the main factors intermediating the health effects of Mediterranean diet on the host. The present perspective discusses the evidences that the Mediterranean diet induces gut microbiome modulation in rodents, non-human primates and human subjects, and discusses the potential role of gut microbiota and microbial metabolites as one of the fundamental catalysts intermediating various beneficial health effects of Mediterranean diet on the host.
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Affiliation(s)
- Ravinder Nagpal
- Division of Internal Medicine - Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
- Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
| | - Carol A. Shively
- Department of Pathology - Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
| | - Thomas C. Register
- Department of Pathology - Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
| | - Suzanne Craft
- Department of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
| | - Hariom Yadav
- Division of Internal Medicine - Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
- Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27101, USA
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35
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Balasubramaniam KN, Beisner BA, Hubbard JA, Vandeleest JJ, Atwill ER, McCowan B. Affiliation and disease risk: social networks mediate gut microbial transmission among rhesus macaques. Anim Behav 2019; 151:131-143. [PMID: 32831349 PMCID: PMC7434028 DOI: 10.1016/j.anbehav.2019.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In social animals, affiliative behaviours bring many benefits, but also costs such as disease risk. The ways in which affiliation may affect the risk of infectious agent transmission remain unclear. Moreover, studies linking variation in affiliative interactions to infectious agent incidence/diversity have speculated that disease transmission may have occurred, rather than revealing that transmission did occur. We address these gaps using the phylogenetics of commensal gut Escherichia coli to determine whether affiliative grooming and huddling social networks mediated microbial transmission among rhesus macaques. We collected behavioural and microbial data from adult macaques across a 12-week period that was split into two 6-week phases to better detect dyadic transmission. We reconstructed undirected social networks from affiliative interactions and reconstructed microbial transmission networks from the pairwise phylogenetic similarity of E. coli pulsotypes from macaques within and across adjacent sampling events. Macaque E. coli pulsotypes were more phylogenetically similar to each other than to environmental isolates, which established a premise for socially mediated transmission. Dyadic grooming and huddling frequencies strongly influenced the likelihood of E. coli transmission during the second data collection phase, but not the first. Macaques that were more central/well connected in both their grooming and huddling networks were also more central in the E. coli transmission networks. Our results confirmed that affiliative grooming and huddling behaviours mediate the transmission of gut microbes among rhesus macaques, particularly among females and high-ranking individuals. The detectability of socially mediated E. coli transmission maybe partially masked by environmental acquisition in males, or by high frequencies of interactions in captivity. Predicting the potential transmission pathways of gastrointestinal parasites and pathogens, our findings add to current knowledge of the coevolutionary relationships between affiliative behaviour and health and may be used to identify 'superspreader' individuals as potential targets for disease control strategies.
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Affiliation(s)
- Krishna N. Balasubramaniam
- Department of Population Health & Reproduction, School
of Veterinary Medicine, University of California, Davis, CA, U.S.A
| | - Brianne A. Beisner
- Department of Population Health & Reproduction, School
of Veterinary Medicine, University of California, Davis, CA, U.S.A
- Neuroscience & Behavior Unit, California National
Primate Research Center, University of California, Davis, CA, U.S.A
| | - Josephine A. Hubbard
- Department of Population Health & Reproduction, School
of Veterinary Medicine, University of California, Davis, CA, U.S.A
- Animal Behavior Graduate Group, University of California,
Davis, CA, U.S.A
| | - Jessica J. Vandeleest
- Department of Population Health & Reproduction, School
of Veterinary Medicine, University of California, Davis, CA, U.S.A
- Neuroscience & Behavior Unit, California National
Primate Research Center, University of California, Davis, CA, U.S.A
| | - Edward R. Atwill
- Department of Population Health & Reproduction, School
of Veterinary Medicine, University of California, Davis, CA, U.S.A
| | - Brenda McCowan
- Department of Population Health & Reproduction, School
of Veterinary Medicine, University of California, Davis, CA, U.S.A
- Neuroscience & Behavior Unit, California National
Primate Research Center, University of California, Davis, CA, U.S.A
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36
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Goodfellow CK, Whitney T, Christie DM, Sicotte P, Wikberg EC, Ting N. Divergence in gut microbial communities mirrors a social group fission event in a black-and-white colobus monkey (Colobus vellerosus). Am J Primatol 2019; 81:e22966. [PMID: 30920682 DOI: 10.1002/ajp.22966] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/11/2019] [Accepted: 02/16/2019] [Indexed: 12/16/2022]
Abstract
Host behavior and social factors have increasingly been implicated in structuring the composition of gut microbial communities. In social animals, distinct microbial communities characterize different social groups across a variety of taxa, although little longitudinal research has been conducted that demonstrates how this divergence occurs. Our study addresses this question by characterizing the gut microbial composition of an African Old World monkey, the black-and-white colobus (Colobus vellerosus), before and after a social group fission event. Gut microbial taxonomic composition of these monkeys was profiled using the V-4 hypervariable region of the bacterial 16S ribosomal RNA gene, and pairwise-relatedness values were calculated for all individuals using 17 short tandem repeat loci and partial pedigree information. The two social groups in this study were found to harbor distinct microbial signatures after the fission event from which they emerged, while these communities were not divergent in the same individuals before this event. Three genera were found to differ in abundance between the two new social groups: Parabacteroides, Coprococcus, and Porphyromonadaceae. Additionally, although this fission happened partially along lines of relatedness, relatedness did not structure the differences that we found. Taken together, this study suggests that distinct gut microbial profiles can emerge in social groups in <1 year and recommends further work into more finely mapping the timescales, causes, and potentially adaptive effects of this recurring trend toward distinct group microbial signatures.
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Affiliation(s)
- Claire K Goodfellow
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.,Department of Biology, University of Oregon, Eugene, Oregon
| | - Tabor Whitney
- Department of Biology, University of Oregon, Eugene, Oregon
| | - Diana M Christie
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.,Department of Anthropology, University of Oregon, Eugene, Oregon
| | - Pascale Sicotte
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Eva C Wikberg
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas
| | - Nelson Ting
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.,Department of Anthropology, University of Oregon, Eugene, Oregon
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37
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Tormoehlen K, Johnson-Walker YJ, Lankau EW, Myint MS, Herrmann JA. Considerations for studying transmission of antimicrobial resistant enteric bacteria between wild birds and the environment on intensive dairy and beef cattle operations. PeerJ 2019; 7:e6460. [PMID: 30834183 PMCID: PMC6397636 DOI: 10.7717/peerj.6460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/15/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Wild birds using livestock facilities for food and shelter may contribute to dissemination of enteric pathogens or antimicrobial resistant bacteria. However, drivers of microbial exchange among wildlife and livestock are not well characterized. Predisposition for acquiring and retaining environmental bacteria may vary among species because of physiologic or behavioral differences, complicating selection of a bacterial model that can accurately characterize microbial connections among hosts of interest. This study compares the prevalence and antibiotic resistance phenotypes of two potential model bacterial organisms isolated from wild birds and their environments. METHODS We compared prevalence and resistance profiles of Escherichia coli and Enterococcus species isolated from environmental swabs and bird feces on a residential control site, a confinement dairy, a pasture-based beef farm, and a confinement beef farm. RESULTS Bird feces at all sites had low-to-moderate prevalence of Escherichia coli (range: 17-47%), despite potential for exposure on farms (range: 63-97%). Few Escherichia coli were isolated from the control environment. Enterococcus faecalis was dominant in birds at both beef farms (62% and 81% of Enterococcus isolates) and low-to-moderately prevalent at the dairy and control sites (29% and 23% of isolates, respectively). Antimicrobial resistance prevalence was higher in farm samples compared to those from the residential control, but distribution of resistant isolates varied between the bacterial genera. Birds on all farms carried resistant Enterococcus at similar rates to that of the environment, but resistance was less common in bird-associated Escherichia coli despite presence of resistant isolates in the farm environment. DISCUSSION Bacterial species studied may affect how readily bacterial exchange among populations is detected. Selection of microbial models must carefully consider both the questions being posed and how findings might influence resulting management decisions.
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Affiliation(s)
- Kristin Tormoehlen
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yvette J. Johnson-Walker
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emily W. Lankau
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Ronin Institute, Montclair, NJ, USA
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Maung San Myint
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John A. Herrmann
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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39
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Perofsky AC, Lewis RJ, Meyers LA. Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals. THE ISME JOURNAL 2019; 13:50-63. [PMID: 30108305 PMCID: PMC6299109 DOI: 10.1038/s41396-018-0251-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/03/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022]
Abstract
The gut microbiomes of mammals appear to mirror their hosts' phylogeny, suggesting host-driven microbial community assembly. Yet, much of this evidence stems from comparative studies of distinct wild or captive populations that lack data for disentangling the relative influences of shared phylogeny and environment. Here, we present phylogenetic and multivariate analyses of gut microbiomes from six sympatric (i.e., co-occurring) mammal species inhabiting a 1-km2 area in western Madagascar-three lemur and three non-primate species-that consider genetic, dietary, and ecological predictors of microbiome functionality and composition. Host evolutionary history, indeed, appears to shape gut microbial patterns among both closely and distantly related species. However, we also find that diet-reliance on leaves versus fruit-is the best predictor of microbiome similarity among closely related lemur species, and that host substrate use-ground versus tree-constrains horizontal transmission via incidental contact with feces, with arboreal species harboring far more distinct communities than those of their terrestrial and semi-terrestrial counterparts.
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Affiliation(s)
- Amanda C Perofsky
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Rebecca J Lewis
- Department of Anthropology, The University of Texas at Austin, Austin, TX, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Santa Fe Institute, Santa Fe, NM, USA
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40
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Cox LA, Olivier M, Spradling-Reeves K, Karere GM, Comuzzie AG, VandeBerg JL. Nonhuman Primates and Translational Research-Cardiovascular Disease. ILAR J 2018; 58:235-250. [PMID: 28985395 DOI: 10.1093/ilar/ilx025] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of morbidity and mortality in the United States. Human epidemiological studies provide challenges for understanding mechanisms that regulate initiation and progression of CVD due to variation in lifestyle, diet, and other environmental factors. Studies describing metabolic and physiologic aspects of CVD, and those investigating genetic and epigenetic mechanisms influencing CVD initiation and progression, have been conducted in multiple Old World nonhuman primate (NHP) species. Major advantages of NHPs as models for understanding CVD are their genetic, metabolic, and physiologic similarities with humans, and the ability to control diet, environment, and breeding. These NHP species are also genetically and phenotypically heterogeneous, providing opportunities to study gene by environment interactions that are not feasible in inbred animal models. Each Old World NHP species included in this review brings unique strengths as models to better understand human CVD. All develop CVD without genetic manipulation providing multiple models to discover genetic variants that influence CVD risk. In addition, as each of these NHP species age, their age-related comorbidities such as dyslipidemia and diabetes are accelerated proportionally 3 to 4 times faster than in humans.In this review, we discuss current CVD-related research in NHPs focusing on selected aspects of CVD for which nonprimate model organism studies have left gaps in our understanding of human disease. We include studies on current knowledge of genetics, epigenetics, calorie restriction, maternal calorie restriction and offspring health, maternal obesity and offspring health, nonalcoholic steatohepatitis and steatosis, Chagas disease, microbiome, stem cells, and prevention of CVD.
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Affiliation(s)
- Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | | | - Genesio M Karere
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - John L VandeBerg
- South Texas Diabetes and Obesity Center, School of Medicine, University of Texas Rio Grande Valley, Edinburg/Harlingen/Brownsville, Texas
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41
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Maki KA, Diallo AF, Lockwood MB, Franks AT, Green SJ, Joseph PV. Considerations When Designing a Microbiome Study: Implications for Nursing Science. Biol Res Nurs 2018; 21:125-141. [PMID: 30409024 DOI: 10.1177/1099800418811639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nurse scientists play an important role in studying complex relationships among human genetics, environmental factors, and the microbiome, all of which can contribute to human health and disease. Therefore, it is essential that they have the tools necessary to execute a successful microbiome research study. The purpose of this article is to highlight important methodological factors for nurse scientists to consider when designing a microbiome study. In addition to considering factors that influence host-associated microbiomes (i.e., microorganisms associated with organisms such as humans, mice, and rats), this manuscript highlights study designs and methods for microbiome analysis. Exemplars are presented from nurse scientists who have incorporated microbiome methods into their program of research. This review is intended to be a resource to guide nursing-focused microbiome research and highlights how study of the microbiome can be incorporated to answer research questions.
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Affiliation(s)
- Katherine A Maki
- 1 Department of Biobehavioral Health Science, College of Nursing, University of Illinois at Chicago, Chicago, IL, USA
| | - Ana F Diallo
- 2 Institute of Inclusion, Inquiry and Innovation, Richmond Health and Wellness Clinics, Virginia Commonwealth University School of Nursing, Richmond, VA, USA
| | - Mark B Lockwood
- 1 Department of Biobehavioral Health Science, College of Nursing, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexis T Franks
- 3 Sensory Science and Metabolism Unit, Biobehavioral Branch, Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Stefan J Green
- 4 Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Paule V Joseph
- 3 Sensory Science and Metabolism Unit, Biobehavioral Branch, Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
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42
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Chen Z, Yeoh YK, Hui M, Wong PY, Chan MCW, Ip M, Yu J, Burk RD, Chan FKL, Chan PKS. Diversity of macaque microbiota compared to the human counterparts. Sci Rep 2018; 8:15573. [PMID: 30349024 PMCID: PMC6197227 DOI: 10.1038/s41598-018-33950-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023] Open
Abstract
Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques (N = 116) and compared the compositions with the healthy communities from Human Microbiome Project. The macaque microbiota was dominated by Bacteroidetes, Firmicutes and Proteobacteria; however, there were marked differences in phylotypes enriched across body sites indicative of strong niche specialization. Compared to human gut microbiota where Bacteroides predominately enriched, the surveyed macaque anal community exhibited increased abundance of Prevotella. In contrast to the conserved human vaginal microbiota extremely dominated by Lactobacillus, the macaque vaginal microbial composition was highly diverse while lactobacilli were rare. A constant decrease of the vaginal microbiota diversity was observed among macaque samples from juvenile, adult without tubectomy, and adult with tubectomy, with the most notable distinction being the enrichment of Halomonas in juvenile and Saccharofermentans in contracepted adults. Both macaque and human oral microbiota were colonized with three most common oral bacterial genera: Streptococcus, Haemophilus and Veillonella, and shared relatively conserved communities to each other. A number of bacteria related to human pathogens were consistently detected in macaques. The findings delineate the range of structure and diversity of microbial communities in a wild macaque population, and enable the application of macaque as an animal model for future characterization of microbes in transmission, genomics and function.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Mamie Hui
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Po Yee Wong
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Martin C W Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D Burk
- Departments of Pediatrics, Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics, Gynecology and Woman's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Francis K L Chan
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China. .,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
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Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S. Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d'Ivoire. THE ISME JOURNAL 2018; 12:2559-2574. [PMID: 29955140 PMCID: PMC6154966 DOI: 10.1038/s41396-018-0166-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/04/2018] [Accepted: 05/11/2018] [Indexed: 12/31/2022]
Abstract
Microbiomes impact a variety of processes including a host's ability to access nutrients and maintain health. While host species differences in microbiomes have been described across ecosystems, little is known about how microbiomes assemble, particularly in the ecological and social contexts in which they evolved. We examined gut microbiome composition in nine sympatric wild non-human primate (NHP) species. Despite sharing an environment and interspecific interactions, individuals harbored unique and persistent microbiomes influenced by host species, social group, and parentage, but surprisingly not by social relationships among members of a social group. We found a branching order of host-species networks constructed using the composition of their microbiomes as characters, which was incongruent with known NHP phylogenetic relationships, with chimpanzees (Pan troglodytes verus) sister to colobines, upon which they regularly prey. In contrast to phylogenetic clustering found in all monkey microbiomes, chimpanzee microbiomes were unique in that they exhibited patterns of phylogenetic overdispersion. This reflects unique ecological processes impacting microbiome composition in chimpanzees and future studies will elucidate the aspects of chimpanzee ecology, life history, and physiology that explain their unique microbiome community structure. Our study of contemporaneous microbiomes of all sympatric diurnal NHP in an ecosystem highlights the diverse dispersal routes shaping these complex communities.
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Affiliation(s)
- Jan F Gogarten
- Department of Biology, McGill University, 855 Sherbrooke Street West, Montreal, QC, H3A2T7, Canada
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - T Jonathan Davies
- Department of Biology, McGill University, 855 Sherbrooke Street West, Montreal, QC, H3A2T7, Canada
| | - Jacquelynn Benjamino
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - Alexander Mielke
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Roger Mundry
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Michael C Nelson
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - Roman M Wittig
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, B.P. 1303, Abidjan 01, Côte d'Ivoire.
| | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Sébastien Calvignac-Spencer
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
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The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas. Sci Rep 2018; 8:14482. [PMID: 30262842 PMCID: PMC6160417 DOI: 10.1038/s41598-018-32759-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/13/2018] [Indexed: 12/22/2022] Open
Abstract
The gut microbiome (GMB) of folivores metabolizes dietary fiber into nutrients, including short-chain fatty acids (SCFAs); however, experiments probing the consequences of foliage quality on host GMBs are lacking. We therefore examined GMB structure and function via amplicon sequencing and Nuclear Magnetic Resonance spectroscopy in 31 captive sifakas (Propithecus coquereli) during dietary manipulations associated with husbandry. Supplementing standard diets with diverse foliage blends, versus with a single plant species, promoted more diverse GMBs, enriched for taxa implicated in plant-fiber metabolism, but depleted in taxa implicated in starch metabolism and bile tolerance. The consumption of diverse blends was associated with greater concentrations of colonic SCFAs. Abundant foliage, via forest access, promoted compositionally distinct and more stable GMBs, but reduced concentrations of SCFAs, possibly reflecting selection of high-quality leaves. In 11 subjects denied forest access, we examined the temporal pace of microbial shifts when supplemental foliage was abruptly switched between diverse blends and single species. The sifaka GMB responded within days, with community diversity and composition closely tracking foliage diversity. By providing experimental evidence that the folivore GMB is sensitive to minor changes in dietary foliage, we reveal the fragility of specialist GMBs, with implications for managing the wellbeing of endangered wildlife.
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45
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Sun B, Gu Z, Wang X, Huffman MA, Garber PA, Sheeran LK, Zhang D, Zhu Y, Xia DP, Li JH. Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana). Am J Primatol 2018; 80:e22880. [PMID: 29893498 DOI: 10.1002/ajp.22880] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022]
Abstract
Recent studies highlight that the gut mycobiota play essential roles in mammalian metabolic and immune systems, but to date we lack information on the forces that naturally shape the gut mycobiota of wild primates. To investigate the contributions of host and environmental factors in the taxonomic variation of the gut mycobiota, we examined the effects of age, sex, and season on the fecal mycobiota in wild-living Tibetan macaques (Macaca thibetana). Using next generation sequencing and a longitudinal set of fecal samples collected over 1 year, we identified a set of core fungal taxa present in the Tibetan macaque's fecal samples. The predominant genera Aspergillus and Penicillium, which promote the digestion of cellulose and hemicellulose in herbivorous mammals, were detected in this study. Similar to humans, we found age and sex effects on the macaques' fecal mycobiota. We also found that both fecal fungal composition and diversity (alpha and beta diversity) varied significantly by season. In particular, the Penicillium enriched mycobiota in summer samples may aid in the digestion of cellulose and hemicellulose present in mature leaves. The high alpha diversity detected in Tibetan macaques' winter fecal samples may facilitate a diet rich in fiber ingested during this season. We propose that the gut mycobiota play an important role in the macaques' ability to adapt to seasonal fluctuations in food availability and nutrient content.
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Affiliation(s)
- Binghua Sun
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
| | - Zhiyuan Gu
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
| | - Xi Wang
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
| | | | - Paul A Garber
- Department of Anthropology and Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Illinois, Urbana
| | - Lori K Sheeran
- Department of Biological Sciences and Primate Behavior Program, Central Washington University, Ellensburg, Washington
| | - Dao Zhang
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
| | - Yong Zhu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, China
| | - Dong-Po Xia
- School of Life Science, Anhui University, Hefei, China
| | - Jin-Hua Li
- School of Resource and Environmental Engineering, Anhui University, Hefei, China.,School of Life Science, Hefei Normal University, Hefei, China
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46
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Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ. The gut microbiome of nonhuman primates: Lessons in ecology and evolution. Am J Primatol 2018; 80:e22867. [PMID: 29862519 DOI: 10.1002/ajp.22867] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 03/23/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023]
Abstract
The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.
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Affiliation(s)
- Jonathan B Clayton
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota.,GreenViet Biodiversity Conservation Center, Son Tra District, Danang, Vietnam.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Andres Gomez
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Animal Science, University of Minnesota, St Paul, Minnesota
| | - Katherine Amato
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Anthropology, Northwestern University, Evanston, Illinois
| | - Dan Knights
- Primate Microbiome Project, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Dominic A Travis
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Ran Blekhman
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Falcon Heights, Minnesota
| | - Rob Knight
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Computer Science & Engineering, UC San Diego, La Jolla, California.,Department of Pediatrics, UC San Diego, La Jolla, California.,Center for Microbiome Innovation, UC San Diego, La Jolla, California
| | - Steven Leigh
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Anthropology, University of Colorado Boulder, Boulder, Colorado.,C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois
| | - Rebecca Stumpf
- Primate Microbiome Project, Minneapolis, Minnesota.,C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois.,Department of Anthropology, University of Illinois, Urbana, Illinois
| | - Tiffany Wolf
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Kenneth E Glander
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Francis Cabana
- Primate Microbiome Project, Minneapolis, Minnesota.,Wildlife Nutrition Centre, Wildlife Reserves Singapore, Singapore
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota.,Primate Microbiome Project, Minneapolis, Minnesota.,University of Minnesota, Mid-Central Research and Outreach Center, Willmar, Minnesota
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47
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Grieneisen LE, Livermore J, Alberts S, Tung J, Archie EA. Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons. Integr Comp Biol 2018; 57:770-785. [PMID: 29048537 DOI: 10.1093/icb/icx046] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e.g., dispersal) predict inter-individual variation in gut microbial alpha and beta diversity. We also tested whether social effects differed for prevalent "core" gut microbial taxa, which are thought to provide primary functions to hosts, versus rare "non-core" microbes, which may represent relatively transient environmental acquisitions. Confirming prior studies, we found that each social group harbored a distinct gut microbial community. These differences included both non-core and core gut microbial taxa, suggesting that these effects are not solely driven by recent gut microbial exposures. Within social groups, close grooming partners had more similar core microbiomes, but not non-core microbiomes, than individuals who rarely groomed each other, even controlling for kinship and diet similarity between grooming partners. Finally, in support of the idea that the gut microbiome can be altered by current social context, we found that the longer an immigrant male had lived in a given social group, the more closely his gut microbiome resembled the gut microbiomes of the group's long-term residents. Together, these results reveal the importance of a host's social context in shaping the gut microbiome and shed new light onto the microbiome-related consequences of male dispersal.
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Affiliation(s)
- Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Josh Livermore
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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48
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Liu X, Fan P, Che R, Li H, Yi L, Zhao N, Garber PA, Li F, Jiang Z. Fecal bacterial diversity of wild Sichuan snub-nosed monkeys (Rhinopithecus roxellana). Am J Primatol 2018; 80:e22753. [PMID: 29635791 DOI: 10.1002/ajp.22753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 01/03/2018] [Accepted: 03/01/2018] [Indexed: 12/12/2022]
Abstract
The gastrointestinal tract of primates harbors a complex microbial community, playing an essential role in the degradation of otherwise indigestible structural carbohydrates. The phylogenetic and functional diversity of the bacterial community in the feces as a surrogate for the gastrointestinal tract of wild Sichuan snub-nosed monkeys (Rhinopithecus roxellana, N = 6) was characterized based on sequence analysis of 16S rRNA genes. A sex comparison was conducted, with a prior hypothesis that the abundances of the bacterial taxa and/or functional categories associated with energy and nutrient metabolism would be higher in adult females (N = 3) due to the higher reproductive costs compared to adult males (N = 3). Ten phyla were identified in all samples, among which Bacteroidetes and Firmicutes were the predominant. Included in the above two phyla, the members of Prevotellaceae (Prevotella in particular) and Ruminococcaceae were highly abundant, which are common bacteria in the gastrointestinal tract of primates and can degrade various structural carbohydrates such as cellulose, hemicellulose, and pectin. This functionality was in line with the high abundances of the metagenomes associated with carbohydrate metabolism. Consistent with our hypothesis, the abundances of the metagenomes associated with energy metabolism, folding/sorting and degradation, glycan biosynthesis and metabolism, and metabolism of amino acids were higher in adult females relative to adult males. Sex differences were also detected in the bacterial community structure, although no sex differences in the proportions of any bacterial taxa were found likely due to the small sample size. These results suggested that gastrointestinal bacterial communities may aid adult females in increasing energy and nutrition utilization efficiencies compared to adult males. Fecal bacterial communities were found to be more similar between individuals in adult females than in adult males. Our study presented the first examination of the fecal bacterial diversity of a little-studied, endangered foregut fermenter.
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Affiliation(s)
- Xuecong Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Penglai Fan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Institute of Ecology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Rongxiao Che
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, Australia
| | - Huan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lina Yi
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Na Zhao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Paul A Garber
- Department of Anthropology, University of Illinois, Urbana, Illinois
| | - Fang Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhigang Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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49
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Kurtz C, Denney WS, Blankstein L, Guilmain SE, Machinani S, Kotula J, Saha S, Miller P, Brennan AM. Translational Development of Microbiome-Based Therapeutics: Kinetics of E. coli Nissle and Engineered Strains in Humans and Nonhuman Primates. Clin Transl Sci 2018; 11:200-207. [PMID: 29194983 PMCID: PMC5866967 DOI: 10.1111/cts.12528] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/09/2017] [Indexed: 12/12/2022] Open
Abstract
Understanding the pharmacology of microbiome-based therapeutics is required to support the development of new medicines. Strains of E. coli Nissle (EcN) were genetically modified and administered to cynomolgus monkeys at doses of 1 × 109 and 1 × 1012 colony-forming units (CFU)/day for 28 days. A clinical study to evaluate the exposure and clearance of EcN in healthy volunteers was also performed. Healthy subjects received oral doses of EcN, 2.5 to 25 × 109 CFU 3 times daily for 28 days or a single day. In cynomolgus monkeys, replicating strains yielded higher fecal concentrations than nonreplicating strains and persisted for longer following cessation of dosing. In the clinical study, all subjects cleared EcN following cessation of dosing with median clearance of 1 week. Quantitative methodology can be applied to microbiome-based therapeutics, and similar kinetics and clearance were observed for EcN in cynomolgus monkeys and humans.
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50
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Balasubramaniam K, Beisner B, Guan J, Vandeleest J, Fushing H, Atwill E, McCowan B. Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques ( Macaca mulatta). PeerJ 2018; 6:e4271. [PMID: 29372120 PMCID: PMC5775753 DOI: 10.7717/peerj.4271] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/27/2017] [Indexed: 01/17/2023] Open
Abstract
In group-living animals, heterogeneity in individuals' social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals' commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques (Macaca mulatta), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals' direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function.
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Affiliation(s)
- Krishna Balasubramaniam
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Brianne Beisner
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Brain, Mind & Behavior, California National Primate Research Center, University of California, Davis, CA, United States of America
| | - Jiahui Guan
- Department of Statistics, University of California, Davis, CA, United States of America
| | - Jessica Vandeleest
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Brain, Mind & Behavior, California National Primate Research Center, University of California, Davis, CA, United States of America
| | - Hsieh Fushing
- Department of Statistics, University of California, Davis, CA, United States of America
| | - Edward Atwill
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Brenda McCowan
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Brain, Mind & Behavior, California National Primate Research Center, University of California, Davis, CA, United States of America
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