1
|
Sariyati NH, Othman N, Abdullah-Fauzi NAF, Chan E, Md-Zain BM, Karuppannan KV, Abdul-Latiff MAB. Characterizing the gastrointestinal microbiome diversity in endangered Malayan Siamang (Symphalangus syndactylus): Insights into group composition, age variability and sex-related patterns. J Med Primatol 2024; 53:e12730. [PMID: 39148344 DOI: 10.1111/jmp.12730] [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] [Received: 04/14/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus. METHODS This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region. RESULTS A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut. CONCLUSIONS This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.
Collapse
Affiliation(s)
- Nur Hartini Sariyati
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Eddie Chan
- Treks Event Sdn Bhd, Lot AW/G5.00, GF, Awana Hotel Genting Highlands Resort, Genting Highlands, Pahang, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| |
Collapse
|
2
|
Osman NA, Gani M, Tingga RCT, Abdul-Latiff MAB, Mohd-Ridwan AR, Chan E, Md-Zain BM. Unveiling the Gut Microbiota of Pig-Tailed Macaque (Macaca nemestrina) in Selected Habitats in Malaysia. J Med Primatol 2024; 53:e12737. [PMID: 39323065 DOI: 10.1111/jmp.12737] [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] [Received: 07/13/2024] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/27/2024]
Abstract
BACKGROUND The gut microbiota plays an important role in primates, which may be associated with their habitat. In Malaysia, pig-tailed macaques (Macaca nemestrina) live in different habitat environments and have traditionally been used for coconut plucking for more than a century. There is currently no information regarding the gut microbiota of this macaque in Malaysia. To address this oversight, this study employed a fecal metabarcoding approach to determine the gut microbiota composition of pig-tailed macaques and establish how these microbial communities correspond with the macaque external environments of residential area, forest edge, and fragmented forest. METHODS To determine this connection, 300 paired-end sequences of 16S rRNA were amplified and sequenced using the MiSeq platform. RESULTS In the pig-tailed macaque fecal samples, we identified 17 phyla, 40 orders, 52 families, 101 genera, and 139 species of bacteria. The most prevalent bacterial families in the gut of pig-tailed macaques were Firmicutes (6.31%) and Proteobacteria (0.69%). Our analysis did not identify a significant difference between the type of environmental habitat and the gut microbiota composition of these macaques. CONCLUSIONS There was great variation in the population richness and bacterial community structure. The abundance of Firmicutes and Proteobacteria helps this macaque digest food more easily while maintaining a healthy gut microbiota diversity. Exploring the gut microbiota provides an initial effort to support pig-tailed macaque conservation in the future.
Collapse
Affiliation(s)
- Nur Azimah Osman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA Cawangan Negeri Sembilan, Kampus Kuala Pilah, Kuala Pilah, Negeri Sembilan, Malaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN) Peninsular Malaysia, Kuala Lumpur, Malaysia
| | - Roberta Chaya Tawie Tingga
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | | | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Eddie Chan
- Genting Nature Adventure, Resorts World Awana Hotel, Pahang, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| |
Collapse
|
3
|
Ren Q, Hill JE. Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants. ISME COMMUNICATIONS 2023; 3:77. [PMID: 37479852 PMCID: PMC10362019 DOI: 10.1038/s43705-023-00283-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/23/2023]
Abstract
The "universal target" region of the gene encoding the 60 kDa chaperonin protein (cpn60, also known as groEL or hsp60) is a proven sequence barcode for bacteria and a useful target for marker gene amplicon-based studies of complex microbial communities. To date, identification of cpn60 sequence variants from microbiome studies has been accomplished by alignment of queries to a reference database. Naïve Bayesian classifiers offer an alternative identification method that provides variable rank classification and shorter analysis times. We curated a set of cpn60 barcode sequences to train the RDP classifier and tested its performance on data from previous human microbiome studies. Results showed that sequences accounting for 79%, 86% and 92% of the observations (read counts) in saliva, vagina and infant stool microbiome data sets were classified to the species rank. We also trained the QIIME 2 q2-feature-classifier on cpn60 sequence data and demonstrated that it gives results consistent with the standalone RDP classifier. Successful implementation of a naïve Bayesian classifier for cpn60 sequences will facilitate future microbiome studies and open opportunities to integrate cpn60 amplicon sequence identification into existing analysis pipelines.
Collapse
Affiliation(s)
- Qingyi Ren
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.
| |
Collapse
|
4
|
Eschweiler K, Clayton JB, Moresco A, McKenney EA, Minter LJ, Suhr Van Haute MJ, Gasper W, Hayer SS, Zhu L, Cooper K, Ange-van Heugten K. Host Identity and Geographic Location Significantly Affect Gastrointestinal Microbial Richness and Diversity in Western Lowland Gorillas ( Gorilla gorilla gorilla) under Human Care. Animals (Basel) 2021; 11:3399. [PMID: 34944176 PMCID: PMC8697915 DOI: 10.3390/ani11123399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/13/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the "normal" state of the GI microbiome composition across multiple host species has gained increasing importance for distinguishing healthy versus diseased states. This study aimed to determine baselines and trends over time to establish "typical" patterns of GI microbial richness and diversity, as well as inter-individual variation, in three populations of western lowland gorillas (Gorilla gorilla gorilla) under human care at three zoological institutions in North America. Fecal samples were collected from 19 western lowland gorillas every two weeks for seven months (n = 248). Host identity and host institution significantly affected GI microbiome community composition (p < 0.05), although host identity had the most consistent and significant effect on richness (p = 0.03) and Shannon diversity (p = 0.004) across institutions. Significant changes in microbial abundance over time were observed only at Denver Zoo (p < 0.05). Our results suggest that individuality contributes to most of the observed GI microbiome variation in the study populations. Our results also showed no significant changes in any individual's microbial richness or Shannon diversity during the 7-month study period. While some microbial taxa (Prevotella, Prevotellaceae and Ruminococcaceae) were detected in all gorillas at varying levels, determining individual baselines for microbial composition comparisons may be the most useful diagnostic tool for optimizing non-human primate health under human care.
Collapse
Affiliation(s)
- Katrina Eschweiler
- Department of Nutrition, Denver Zoo, Denver, CO 80205, USA;
- Department of Animal Science, NC State University, Raleigh, NC 27695, USA
| | - Jonathan B. Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (J.B.C.); (S.S.H.)
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Anneke Moresco
- Department of Animal Welfare and Research, Denver Zoo, Denver, CO 80205, USA;
- Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA;
| | - Erin A. McKenney
- Department of Applied Ecology, NC State University, Raleigh, NC 27695, USA;
| | - Larry J. Minter
- Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA;
- Hanes Veterinary Medical Center, North Carolina Zoo, Asheboro, NC 27205, USA
| | - Mallory J. Suhr Van Haute
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - William Gasper
- College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, USA;
| | - Shivdeep Singh Hayer
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (J.B.C.); (S.S.H.)
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.Z.); (K.C.)
| | - Kathryn Cooper
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.Z.); (K.C.)
| | | |
Collapse
|
5
|
Mallott EK, Amato KR. Butyrate-production pathway abundances are similar in human and nonhuman primate gut microbiomes. Mol Biol Evol 2021; 39:6372698. [PMID: 34542625 PMCID: PMC8763029 DOI: 10.1093/molbev/msab279] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Over the course of human evolution, shifts in dietary practices such as meat-eating and cooking, have resulted in reduced fiber intake, a trend that has been exaggerated more recently in industrialized populations. Reduced fiber consumption is associated with a loss of gut microbial taxa that degrade fiber, particularly butyrate. Therefore, this dietary shift in humans may have altered the abundance of microbial genes involved in butyrate production. This study uses a gene-targeted alignment approach to quantify the abundance of butyrate production pathway genes from published wild nonhuman primate and human gut metagenomes. Surprisingly, humans have higher diversity and relative abundances of butyrate production pathways compared with all groups of nonhuman primates except cercopithecoids. Industrialized populations of humans also differ only slightly in butyrate pathway abundance from nonindustrialized populations. This apparent resilience of butyrate production pathways to shifts in human diet across both evolutionary and modern populations may signal an evolutionary shift in host–microbe interactions in humans that increased SCFA production. Such a shift could have contributed to meeting the increased energy requirements of humans relative to nonhuman primates.
Collapse
Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208, USA;
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208, USA;
| |
Collapse
|
6
|
CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems. Microorganisms 2021; 9:microorganisms9040816. [PMID: 33924343 PMCID: PMC8069376 DOI: 10.3390/microorganisms9040816] [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: 03/19/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.
Collapse
|
7
|
Li X, Trivedi U, Brejnrod AD, Vestergaard G, Mortensen MS, Bertelsen MF, Sørensen SJ. The microbiome of captive hamadryas baboons. Anim Microbiome 2020; 2:25. [PMID: 33499948 PMCID: PMC7807707 DOI: 10.1186/s42523-020-00040-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/30/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The hamadryas baboon (Papio hamadryas) is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. In contrast to the widely studied human microbiome, there is a paucity of information on the host-associated microbiomes of nonhuman primates (NHPs). Here, our goal was to understand the microbial composition throughout different body sites of cohabiting baboons. RESULTS We analyzed 170 oral, oropharyngeal, cervical, uterine, vaginal, nasal and rectal samples from 16 hamadryas baboons via 16S rRNA gene sequencing. Additionally, raw Miseq sequencing data from 1041 comparable publicly available samples from the human oral cavity, gut and vagina were reanalyzed using the same pipeline. We compared the baboon and human microbiome of the oral cavity, gut and vagina, showing that the baboon microbiome is distinct from the human. Baboon cohabitants share similar microbial profiles in their cervix, uterus, vagina, and gut. The oral cavity, gut and vagina shared more bacterial amplicon sequence variants (ASVs) in group living baboons than in humans. The shared ASVs had significantly positive correlations between most body sites, suggesting a potential bacterial exchange throughout the body. No significant differences in gut microbiome composition were detected within the maternity line and between maternity lines, suggesting that the offspring gut microbiota is shaped primarily through bacterial exchange among cohabitants. Finally, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in the baboon gut. CONCLUSIONS This study is the first to provide comprehensive analyses of the baboon microbiota across different body sites. We contrast this to human body sites and find substantially different microbiomes. This group of cohabitating baboons generally showed higher microbial diversity and remarkable similarities between body sites than were observed in humans. These data and findings from one group of baboons can form the basis of future microbiome studies in baboons and be used as a reference in research where the microbiome is expected to impact human modeling with baboons.
Collapse
Affiliation(s)
- Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Asker Daniel Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Gisle Vestergaard
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Martin Steen Mortensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000, Frederiksberg, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.
| |
Collapse
|
8
|
Vancuren SJ, Dos Santos SJ, Hill JE. Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. PLoS One 2020; 15:e0235682. [PMID: 32645030 PMCID: PMC7347135 DOI: 10.1371/journal.pone.0235682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.
Collapse
Affiliation(s)
- Sarah J Vancuren
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Scott J Dos Santos
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | |
Collapse
|
9
|
Rifkin RF, Vikram S, Ramond JB, Rey-Iglesia A, Brand TB, Porraz G, Val A, Hall G, Woodborne S, Le Bailly M, Potgieter M, Underdown SJ, Koopman JE, Cowan DA, Van de Peer Y, Willerslev E, Hansen AJ. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome. MICROBIOME 2020; 8:62. [PMID: 32375874 PMCID: PMC7204047 DOI: 10.1186/s40168-020-00832-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
Collapse
Affiliation(s)
- Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Tina B Brand
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Guillaume Porraz
- CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
| | - Aurore Val
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Stephan Woodborne
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
- iThemba LABS, Braamfontein Johannesburg, South Africa
| | - Matthieu Le Bailly
- University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Yves Van de Peer
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- VIB Centre for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Eske Willerslev
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anders J Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark.
| |
Collapse
|
10
|
Sherwin E, Bordenstein SR, Quinn JL, Dinan TG, Cryan JF. Microbiota and the social brain. Science 2019; 366:366/6465/eaar2016. [DOI: 10.1126/science.aar2016] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sociability can facilitate mutually beneficial outcomes such as division of labor, cooperative care, and increased immunity, but sociability can also promote negative outcomes, including aggression and coercion. Accumulating evidence suggests that symbiotic microorganisms, specifically the microbiota that reside within the gastrointestinal system, may influence neurodevelopment and programming of social behaviors across diverse animal species. This relationship between host and microbes hints that host-microbiota interactions may have influenced the evolution of social behaviors. Indeed, the gastrointestinal microbiota is used by certain species as a means to facilitate communication among conspecifics. Further understanding of how microbiota influence the brain in nature may be helpful for elucidating the causal mechanisms underlying sociability and for generating new therapeutic strategies for social disorders in humans, such as autism spectrum disorders (ASDs).
Collapse
Affiliation(s)
- Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN, USA
| | - John L. Quinn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Sciences, University College Cork, Cork, Ireland
| | - John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| |
Collapse
|
11
|
Li X, Rensing C, Taylor WL, Costelle C, Brejnrod AD, Ferry RJ, Higgins PB, Folli F, Kottapalli R, Hubbard GB, Dick EJ, Yooseph S, Nelson KE, Schlabritz-Loutsevitch N. Papio spp. Colon microbiome and its link to obesity in pregnancy. J Med Primatol 2018; 47:393-401. [PMID: 30039863 PMCID: PMC6430121 DOI: 10.1111/jmp.12366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/16/2018] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Gut microbial communities are critical players in the pathogenesis of obesity. Pregnancy is associated with increased bacterial load and changes in gut bacterial diversity. Sparse data exist regarding composition of gut microbial communities in obesity combined with pregnancy. MATERIAL AND METHODS Banked tissues were collected under sterile conditions during necropsy, from three non-obese (nOb) and four obese (Ob) near-term pregnant baboons. Sequences were assigned taxonomy using the Ribosomal Database Project classifier. Microbiome abundance and its difference between distinct groups were assessed by a nonparametric test. RESULTS Three families predominated in both the nOb and Ob colonic microbiome: Prevotellaceae (25.98% and 32.71% respectively), Ruminococcaceae (12.96% and 7.48%), and Lachnospiraceae (8.78% and 11.74%). Seven families of the colon microbiome displayed differences between Ob and nOb groups. CONCLUSION Changes in gut microbiome in pregnant obese animals open the venue for dietary manipulation in pregnancy.
Collapse
Affiliation(s)
- XuanJi Li
- Department of Biology, University of Copenhagen, Universitetsparken, Denmark
| | - Christopher Rensing
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- J. Craig Venter Institute, La Jolla, CA, USA
| | - William L. Taylor
- Molecular Resource Center University of Tennessee Health Science Center, Memphis, TN, USA
| | - Caitlin Costelle
- Molecular Resource Center University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Robert J. Ferry
- Psychology Department, University of Memphis, Memphis, TN, USA
| | | | | | - Rao Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, TX, USA
| | - Gene B. Hubbard
- University of Texas Health Sciences Center at San Antonio, San Antonio, TX, USA
| | - Edward J. Dick
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shibu Yooseph
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | | | - Natalia Schlabritz-Loutsevitch
- Department of Obstetrics and Gynecology, College of Medicine, Texas Tech University Health Sciences Center at the Permian Basin, Odessa, TX, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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: 15] [Impact Index Per Article: 2.5] [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.
Collapse
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
| |
Collapse
|
14
|
The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women. Sci Rep 2017; 7:9212. [PMID: 28835692 PMCID: PMC5569030 DOI: 10.1038/s41598-017-07790-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/04/2017] [Indexed: 01/02/2023] Open
Abstract
The vaginal microbiome plays an important role in maternal and neonatal health. Imbalances in this microbiota (dysbiosis) during pregnancy are associated with negative reproductive outcomes, such as pregnancy loss and preterm birth, but the underlying mechanisms remain poorly understood. Consequently a comprehensive understanding of the baseline microbiome in healthy pregnancy is needed. We characterized the vaginal microbiomes of healthy pregnant women at 11–16 weeks of gestational age (n = 182) and compared them to those of non-pregnant women (n = 310). Profiles were created by pyrosequencing of the cpn60 universal target region. Microbiome profiles of pregnant women clustered into six Community State Types: I, II, III, IVC, IVD and V. Overall microbiome profiles could not be distinguished based on pregnancy status. However, the vaginal microbiomes of women with healthy ongoing pregnancies had lower richness and diversity, lower prevalence of Mycoplasma and Ureaplasma and higher bacterial load when compared to non-pregnant women. Lactobacillus abundance was also greater in the microbiomes of pregnant women with Lactobacillus-dominated CSTs in comparison with non-pregnant women. This study provides further information regarding characteristics of the vaginal microbiome of low-risk pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.
Collapse
|
15
|
Pérez-López E, Rodríguez-Martínez D, Olivier CY, Luna-Rodríguez M, Dumonceaux TJ. Molecular diagnostic assays based on cpn60 UT sequences reveal the geographic distribution of subgroup 16SrXIII-(A/I)I phytoplasma in Mexico. Sci Rep 2017; 7:950. [PMID: 28424530 PMCID: PMC5430490 DOI: 10.1038/s41598-017-00895-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/16/2017] [Indexed: 01/31/2023] Open
Abstract
Geographically diverse samples from strawberry exhibiting symptoms of Strawberry Green Petal (SbGP), periwinkle plants with virescence, and blackberry, blueberry, and raspberry plants displaying yellowing and inedible fruits, were assayed for the presence of phytoplasma DNA. PCR targeting the 16S rRNA-encoding gene and chaperonin-60 (cpn60) showed that the plants were infected with phytoplasma subgroup16SrXIII-(A/I)I (SbGP/MPV). To examine the geographic distribution of this pathogen in Mexico, we designed an array of cpn60-targeted molecular diagnostic assays for SbGP/MPV phytoplasma. A fluorescent microsphere hybridization assay was designed that was capable of detecting SbGP/MPV phytoplasma in infected plant tissues, successfully differentiating it from other known phytoplasma cpn60 UT sequences, while identifying a double infection with SbGP/MPV and aster yellows (16SrI) phytoplasma. Two quantitative assays, quantitative real-time PCR (qRT-PCR) and droplet digital PCR (ddPCR), gave similar results in infected samples. Finally, a loop-mediated isothermal amplification (LAMP) assay provided rapid detection of SbGP/MPV phytoplasma DNA. Application of these assays revealed that SbGP/MPV phytoplasma is widely distributed in Central Mexico, with positive samples identified from eleven localities within three states separated by hundreds of kilometres. These results also provide tools for determining the presence and geographic distribution of this pathogen in plant and insect samples in other localities.
Collapse
Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, Mexico
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | | | - Chrystel Y Olivier
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Mauricio Luna-Rodríguez
- Laboratorio de Genética e Interacciones Planta Microorganismos, Facultad de Ciencias Agrícolas, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Tim J Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada.
| |
Collapse
|
16
|
Pérez-López E, Dumonceaux TJ. Detection and identification of the heterogeneous novel subgroup 16SrXIII-(A/I)I phytoplasma associated with strawberry green petal disease and Mexican periwinkle virescence. Int J Syst Evol Microbiol 2016; 66:4406-4415. [DOI: 10.1099/ijsem.0.001365] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas, Xalapa, Veracruz, Mexico
| | - Tim J. Dumonceaux
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
17
|
McKenney EA, Rodrigo A, Yoder AD. Patterns of gut bacterial colonization in three primate species. PLoS One 2015; 10:e0124618. [PMID: 25970595 PMCID: PMC4430486 DOI: 10.1371/journal.pone.0124618] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/03/2015] [Indexed: 01/15/2023] Open
Abstract
Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.
Collapse
Affiliation(s)
- Erin A. McKenney
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Allen Rodrigo
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Duke Lemur Center, Duke University, Durham, North Carolina, United States of America
| |
Collapse
|