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Ashique S, Mohanto S, Ahmed MG, Mishra N, Garg A, Chellappan DK, Omara T, Iqbal S, Kahwa I. Gut-brain axis: A cutting-edge approach to target neurological disorders and potential synbiotic application. Heliyon 2024; 10:e34092. [PMID: 39071627 PMCID: PMC11279763 DOI: 10.1016/j.heliyon.2024.e34092] [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: 03/27/2024] [Revised: 06/10/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
The microbiota-gut-brain axis (MGBA) represents a sophisticated communication network between the brain and the gut, involving immunological, endocrinological, and neural mediators. This bidirectional interaction is facilitated through the vagus nerve, sympathetic and parasympathetic fibers, and is regulated by the hypothalamic-pituitary-adrenal (HPA) axis. Evidence shows that alterations in gut microbiota composition, or dysbiosis, significantly impact neurological disorders (NDs) like anxiety, depression, autism, Parkinson's disease (PD), and Alzheimer's disease (AD). Dysbiosis can affect the central nervous system (CNS) via neuroinflammation and microglial activation, highlighting the importance of the microbiota-gut-brain axis (MGBA) in disease pathogenesis. The microbiota influences the immune system by modulating chemokines and cytokines, impacting neuronal health. Synbiotics have shown promise in treating NDs by enhancing cognitive function and reducing inflammation. The gut microbiota's role in producing neurotransmitters and neuroactive compounds, such as short-chain fatty acids (SCFAs), is critical for CNS homeostasis. Therapeutic interventions targeting the MGBA, including dietary modulation and synbiotic supplementation, offer potential benefits for managing neurodegenerative disorders. However, more in-depth clinical studies are necessary to fully understand and harness the therapeutic potential of the MGBA in neurological health and disease.
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Affiliation(s)
- Sumel Ashique
- Department of Pharmaceutical Sciences, Bengal College of Pharmaceutical Sciences & Research, Durgapur, 713212, West Bengal, India
| | - Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Neeraj Mishra
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior, MP, 474005, India
| | - Ashish Garg
- Department of Pharmaceutics, Guru Ramdas Khalsa Institute of Science and Technology (Pharmacy), Jabalpur, Madhya Pradesh, India
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Timothy Omara
- Department of Chemistry, College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Shabnoor Iqbal
- African Medicines Innovations and Technologies Development, Department of Pharmacology, Faculty of Health Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | - Ivan Kahwa
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Uganda
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Pfau M, Degregori S, Johnson G, Tennenbaum SR, Barber PH, Philson CS, Blumstein DT. The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231305. [PMID: 37830026 PMCID: PMC10565414 DOI: 10.1098/rsos.231305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
The gut microbiome has a well-documented relationship with host fitness. Greater microbial diversity and abundance of specific microbes have been associated with improved fitness outcomes. Intestinal microbes also may be associated with patterns of social behaviour. However, these associations have been largely studied in captive animal models; we know less about microbiome composition as a potential driver of individual social behaviour and position in the wild. We used linear mixed models to quantify the relationship between fecal microbial composition, diversity and social network traits in a wild population of yellow-bellied marmots (Marmota flaviventer). We focused our analyses on microbes previously linked to sociability and neurobehavioural alterations in captive rodents, primates and humans. Using 5 years of data, we found microbial diversity (Shannon-Wiener and Faith's phylogenetic diversity) has a modest yet statistically significant negative relationship with the number of social interactions an individual engaged in. We also found a negative relationship between Streptococcus spp. relative abundance and two social network measures (clustering coefficient and embeddedness) that quantify an individual's position relative to others in their social group. These findings highlight a potentially consequential relationship between microbial composition and social behaviour in a wild social mammal.
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Affiliation(s)
- Madison Pfau
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Sam Degregori
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Gina Johnson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Stavi R. Tennenbaum
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Conner S. Philson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
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Khairulmunir M, Gani M, Karuppannan KV, Mohd-Ridwan AR, Md-Zain BM. High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger ( Pantheratigrisjacksoni) during fasting. Biodivers Data J 2023; 11:e104757. [PMID: 37711366 PMCID: PMC10498273 DOI: 10.3897/bdj.11.e104757] [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: 04/09/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (PERHILITAN), KM 10 Jalan CherasKuala LumpurMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota SamarahanMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
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4
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Safika S, Indrawati A, Afiff U, Hastuti YT, Zureni Z, Jati AP. First Study on profiling of gut microbiome in wild and captive Sumatran orangutans ( Pongo abelii). Vet World 2023; 16:717-727. [PMID: 37235163 PMCID: PMC10206964 DOI: 10.14202/vetworld.2023.717-727] [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] [Accepted: 02/27/2023] [Indexed: 05/28/2023] Open
Abstract
Background and Aim Orangutans are an "umbrella species" for conserving tropical forests in Sumatra and Kalimantan. There are remarkable changes between the gut microbiomes of wild and captive Sumatran orangutans. This study aimed to profile gut microbiota of wild and captive Sumatran orangutans. Materials and Methods Nine fecal samples collected from wild orangutans and nine fecal samples collected from captive orangutans were divided into three replicates. Each replicate randomly combined three pieces and were analyzed on the Illumina platform. A bioinformatics study of 16S rRNA according to Qiime2 (Version 2021.4) and microbiome profiling analysis was conducted. Results The relative abundance of different microbial taxa varied significantly between wild and captive Sumatran orangutans. Among the operational taxonomic units, various proportions of Firmicutes, Proteobacteria, Bacteroidetes, Euryarchaeota, Acidobacteria, Actinobacteria and Verrucomicrobia predominated. Solobacterium was found only in 19% of captive orangutans. Methanobrevibacter was identified to be prevalent among wild orangutans (16%). Analysis of the core microbiome from the combined wild and captive data revealed seven species as cores. According to linear discriminant analysis effect size, Micrococcus luteus, Bacteroidescaccae, Lachnospiraceae bacterium, Ruthenibacterium lactatiformans, Haemophilus haemolyticus, and Chishuiella spp. were microbiome biomarkers in captive orangutans, whereas Roseburia inulinivorans, Collinsella aerofaciens, Oscillibacter spp., and Eubacterium hallii were microbiome biomarkers in wild orangutans. Conclusion There were differences in the microbiome biomarkers of wild and captive Sumatran orangutans. This study is important for understanding the role of gut bacteria in the health of Sumatran orangutans.
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Affiliation(s)
- Safika Safika
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Agustin Indrawati
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Usamah Afiff
- Division of Medical Microbiology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | | | - Zureni Zureni
- Class II Agricultural Quarantine Center Medan, Indonesia
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Lan LY, Hong QX, Gao SM, Li Q, You YY, Chen W, Fan PF. Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health. Am J Primatol 2023; 85:e23468. [PMID: 36691713 DOI: 10.1002/ajp.23468] [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: 04/05/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
The gut microbiota plays an integral role in the metabolism and immunity of animal hosts, and provides insights into the health and habitat assessment of threatened animals. The skywalker hoolock gibbon (Hoolock tianxing) is a newly described gibbon species, and is considered an endangered species. Here, we used 16S rRNA amplicon sequencing to describe the fecal bacterial community of skywalker hoolock gibbons from different habitats and in captivity. Fecal samples (n = 5) from two captive gibbons were compared with wild populations (N = 6 gibbons, n = 33 samples). At the phylum level, Spirochetes, Proteobacteria, Firmicutes, Bacteroidetes dominated in captive gibbons, while Firmicutes, Bacteroidetes, and Tenericutes dominated in wild gibbons. At the genus level, captive gibbons were dominated by Treponema-2, followed by Succinivibrio and Cerasicoccus, while wild gibbons were dominated by Anaeroplasma, Prevotellaceae UCG-001, and Erysipelotrichaceae UCG-004. Captive rearing was significantly associated with lower taxonomic alpha-diversity, and different relative abundance of some dominant bacteria compared to wild gibbons. Predicted Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that captive gibbons have significantly lower total pathway diversity and higher relative abundance of bacterial functions involved in "drug resistance: antimicrobial" and "carbohydrate metabolism" than wild gibbons. This study reveals the potential influence of captivity and habitat on the gut bacterial community of gibbons and provides a basis for guiding the conservation management of captive populations.
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Affiliation(s)
- Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Xuan Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu-Yan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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6
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Fenn J, Taylor C, Goertz S, Wanelik KM, Paterson S, Begon M, Jackson J, Bradley J. Discrete patterns of microbiome variability across timescales in a wild rodent population. BMC Microbiol 2023; 23:87. [PMID: 36997846 PMCID: PMC10061908 DOI: 10.1186/s12866-023-02824-x] [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: 08/22/2022] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Mammalian gastrointestinal microbiomes are highly variable, both within individuals and across populations, with changes linked to time and ageing being widely reported. Discerning patterns of change in wild mammal populations can therefore prove challenging. We used high-throughput community sequencing methods to characterise the microbiome of wild field voles (Microtus agrestis) from faecal samples collected across 12 live-trapping field sessions, and then at cull. Changes in α- and β-diversity were modelled over three timescales. Short-term differences (following 1–2 days captivity) were analysed between capture and cull, to ascertain the degree to which the microbiome can change following a rapid change in environment. Medium-term changes were measured between successive trapping sessions (12–16 days apart), and long-term changes between the first and final capture of an individual (from 24 to 129 days). The short period between capture and cull was characterised by a marked loss of species richness, while over medium and long-term in the field, richness slightly increased. Changes across both short and long timescales indicated shifts from a Firmicutes-dominant to a Bacteroidetes-dominant microbiome. Dramatic changes following captivity indicate that changes in microbiome diversity can be rapid, following a change of environment (food sources, temperature, lighting etc.). Medium- and long-term patterns of change indicate an accrual of gut bacteria associated with ageing, with these new bacteria being predominately represented by Bacteroidetes. While the patterns of change observed are unlikely to be universal to wild mammal populations, the potential for analogous shifts across timescales should be considered whenever studying wild animal microbiomes. This is especially true if studies involve animal captivity, as there are potential ramifications both for animal health, and the validity of the data itself as a reflection of a ‘natural’ state of an animal.
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Affiliation(s)
- Jonathan Fenn
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Christopher Taylor
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Sarah Goertz
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klara M. Wanelik
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Steve Paterson
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Mike Begon
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Joe Jackson
- grid.8752.80000 0004 0460 5971University of Salford, Salford, UK
| | - Jan Bradley
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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Sawada A, Hayakawa T, Kurihara Y, Lee W, Hanya G. Seasonal responses and host uniqueness of gut microbiome of Japanese macaques in lowland Yakushima. Anim Microbiome 2022; 4:54. [PMID: 36163043 PMCID: PMC9513907 DOI: 10.1186/s42523-022-00205-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Background Changes in the gut microbial composition is an important response to cope with the seasonal fluctuations in the environment such as food availability. We examined the bacterial gut microbiome of the wild nonhuman primate, Japanese macaque (Macaca fuscata) in Yakushima over 13 months by noninvasive continuous sampling from three identified adult females. Results Dietary composition varied considerably over the study period and displayed marked shifts with the seasons. Feeding of leaves, fruits, and invertebrates were their main foods for at least one month. Diet had a significant influence on the gut microbiome. We also confirmed significant effect of host uniqueness in the gut microbiome among the three macaques. Leaf-dominated diet shaped unique gut microbiome structures where the macaques had the highest alpha diversity and their gut microbiome was enriched with Spirochaetes and Tenericutes. Diet-related differences in the putative function were detected, such as a differentially abundant urea cycle during the leaf-feeding season. Conclusion Both diet and host individuality exerted similar amounts of effect on gut microbe community composition. Major bacterial taxa showed a similar response to monthly fluctuations of fruit and invertebrate feeding, which was largely opposite to that of leaf feeding. The main constituents of fruits and invertebrates are both digestible with the enzyme of the host animals, but that of leaves is not available as an energy source without the aid of the fermentation of the gut microbiome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00205-9.
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Kitrinos C, Bell RB, Bradley BJ, Kamilar JM. Hair Microbiome Diversity within and across Primate Species. mSystems 2022; 7:e0047822. [PMID: 35876529 PMCID: PMC9426569 DOI: 10.1128/msystems.00478-22] [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: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces. While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome. Here, we collected hair samples (n = 158) from 8 body sites across 12 NHP species housed at three zoological institutions in the United States to examine the following: (1) the diversity and composition of the primate hair microbiome and (2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we expect significant differences in microbiome diversity across host body sites, sexes, institutions, and species. We found our samples contained high abundances of gut-, respiratory-, and environment-associated microbiota. In addition, multiple factors predicted microbiome diversity and composition, although host species identity outweighed sex, body site, and institution as the strongest predictor. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites, which differs from the human condition. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome. IMPORTANCE We created the most comprehensive primate hair and skin data set to date, including data from 12 nonhuman primate species sampled from 8 body regions each. We find that the nonhuman primate hair microbiome is distinct from the human hair and skin microbiomes in that it is relatively uniform-as opposed to distinct-across body regions and is most abundant in gut-, environment-, and respiratory-associated microbiota rather than human skin-associated microbiota. Furthermore, we found that the nonhuman primate hair microbiome varies with host species identity, host sex, host environment, and host body site, with host species identity being the strongest predictor. This result demonstrates that nonhuman primate hair microbiome diversity varies with both evolutionary and environmental factors and within and across primate species. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome.
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Affiliation(s)
- Catherine Kitrinos
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Rachel B. Bell
- Graduate Program in Organismic and Evolution Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Brenda J. Bradley
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Jason M. Kamilar
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, USA
- Graduate Program in Organismic and Evolution Biology, University of Massachusetts, Amherst, Massachusetts, USA
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10
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Jia T, Chang WS, Marcelino VR, Zhao S, Liu X, You Y, Holmes EC, Shi M, Zhang C. Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. Front Vet Sci 2022; 8:778556. [PMID: 35141306 PMCID: PMC8819141 DOI: 10.3389/fvets.2021.778556] [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: 10/08/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Rhesus macaques (Macaca mulatta) are the most widely distributed species of Old World monkey and are frequently used as animal models to study human health and disease. Their gastrointestinal microbial community likely plays a major role in their physiology, ecology and evolution. Herein, we compared the fecal microbiome and antibiotic resistance genes in 15 free-ranging and 81 zoo-captive rhesus macaques sampled from two zoos in China, using both 16S amplicon sequencing and whole genome shotgun DNA sequencing approaches. Our data revealed similar levels of microbial diversity/richness among the three groups, although the composition of each group differed significantly and were particularly marked between the two zoo-captive and one wild groups. Zoo-captive animals also demonstrated a greater abundance and diversity of antibiotic genes. Through whole genome shotgun sequencing we also identified a mammalian (simian) associated adenovirus. Overall, this study provides a comprehensive analysis of resistomes and microbiomes in zoo-captive and free-ranging monkeys, revealing that semi-captive wildlife might harbor a higher diversity of antimicrobial resistant genes.
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Affiliation(s)
- Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- *Correspondence: Wei-Shan Chang
| | - Vanessa R. Marcelino
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Sufen Zhao
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
- Mang Shi
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
- Chenglin Zhang
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11
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Chiang E, Deblois CL, Carey HV, Suen G. Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Anim Microbiome 2022; 4:1. [PMID: 34980290 PMCID: PMC8722175 DOI: 10.1186/s42523-021-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. RESULTS Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. CONCLUSIONS This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
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Affiliation(s)
- Edna Chiang
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Courtney L. Deblois
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hannah V. Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Garret Suen
- Present Address: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
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12
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Diaz J, Reese AT. Possibilities and limits for using the gut microbiome to improve captive animal health. Anim Microbiome 2021; 3:89. [PMID: 34965885 PMCID: PMC8715647 DOI: 10.1186/s42523-021-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022] Open
Abstract
Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.
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Affiliation(s)
- Jessica Diaz
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Aspen T Reese
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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13
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Houtz JL, Sanders JG, Denice A, Moeller AH. Predictable and host-species specific humanization of the gut microbiota in captive primates. Mol Ecol 2021; 30:3677-3687. [PMID: 34013536 PMCID: PMC10039810 DOI: 10.1111/mec.15994] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Humans and nonhuman primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts' phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here, we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs' gut microbial clades based on the propensity of their lineages to be lost or replaced in captivity by lineages found in humans. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.
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Affiliation(s)
- Jennifer L. Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anthony Denice
- Project Chimps, Blue Ridge, GA, USA
- Chimpanzee Sanctuary Northwest, Cle Elum, WA, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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14
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Jiang D, He X, Valitutto M, Chen L, Xu Q, Yao Y, Hou R, Wang H. Gut microbiota composition and metabolomic profiles of wild and captive Chinese monals (Lophophorus lhuysii). Front Zool 2020; 17:36. [PMID: 33292307 PMCID: PMC7713318 DOI: 10.1186/s12983-020-00381-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains in southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. RESULTS The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations between metabolite types and bacterial genus were detected. CONCLUSIONS There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.
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Affiliation(s)
- Dandan Jiang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Xin He
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Marc Valitutto
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
- EcoHealth Alliance, New York, NY, 10012, USA
| | - Li Chen
- Sichuan Fengtongzhai National Nature reserve administration, Yaan, 625700, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.
- Sichuan Academy of Giant Panda, Chengdu, 610081, China.
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15
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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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16
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Duperron S, Halary S, Gallet A, Marie B. Microbiome-Aware Ecotoxicology of Organisms: Relevance, Pitfalls, and Challenges. Front Public Health 2020; 8:407. [PMID: 32974256 PMCID: PMC7472533 DOI: 10.3389/fpubh.2020.00407] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/09/2020] [Indexed: 01/16/2023] Open
Abstract
Over the last 15 years, the advent of high-throughput "omics" techniques has revealed the multiple roles and interactions occurring among hosts, their microbial partners and their environment. This microbiome revolution has radically changed our views of biology, evolution, and individuality. Sitting at the interface between a host and its environment, the microbiome is a relevant yet understudied compartment for ecotoxicology research. Various recent works confirm that the microbiome reacts to and interacts with contaminants, with consequences for hosts and ecosystems. In this paper, we thus advocate for the development of a "microbiome-aware ecotoxicology" of organisms. We emphasize its relevance and discuss important conceptual and technical pitfalls associated with study design and interpretation. We identify topics such as functionality, quantification, temporality, resilience, interactions, and prediction as major challenges and promising venues for microbiome research applied to ecotoxicology.
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Affiliation(s)
- Sébastien Duperron
- Muséum National d'Histoire Naturelle, CNRS, UMR7245 Mécanismes de Communication et Adaptation des Micro-organismes, Paris, France.,Institut Universitaire de France, Paris, France
| | - Sébastien Halary
- Muséum National d'Histoire Naturelle, CNRS, UMR7245 Mécanismes de Communication et Adaptation des Micro-organismes, Paris, France
| | - Alison Gallet
- Muséum National d'Histoire Naturelle, CNRS, UMR7245 Mécanismes de Communication et Adaptation des Micro-organismes, Paris, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, CNRS, UMR7245 Mécanismes de Communication et Adaptation des Micro-organismes, Paris, France
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17
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Kobayashi A, Tsuchida S, Hattori T, Ogata K, Ueda A, Yamada T, Murata K, Nakamura H, Ushida K. Metabolomic LC-MS/MS analyses and meta 16S rRNA gene analyses on cecal feces of Japanese rock ptarmigans reveal fundamental differences between semi-wild and captive raised individuals. J Vet Med Sci 2020; 82:1165-1172. [PMID: 32581149 PMCID: PMC7468055 DOI: 10.1292/jvms.20-0003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ex situ conservation of Japanese rock ptarmigans began in 2015 with the aim of reintroducing artificially raised birds into their original habitat. However, the current raising method in captivity seems insufficient in terms of the survivability of artificially raised birds in natural conditions. Feeding management is one potential reason for such insufficiency. In this study, we performed a comprehensive analysis of the hydrophilic metabolites by LC-MS/MS for the cecal feces of Japanese rock ptarmigans under in situ and ex situ conservation to reveal their gut chemical environment. We also analyzed the developmental processes of cecal microbiomes both in situ semi-wild and ex situ captive individuals. Metabolites of nucleic acid were rich in the in situ individuals, and free amino acids were rich in the ex situ individuals. The differences in the microbiome composition between in situ and ex situ individuals were also pronounced; major genera of in situ individuals were not detected or few in ex situ individuals. The alpha diversity of the cecal microbiome of semi-wild chicks at 1 week of age was almost the same as that of their hens, while it was very low in captive individuals. Sub-therapeutic use of oxytetracycline, a diet rich in protein and energy, and isolation from adult birds are considered to be causes for these great differences in gut chemical and microbiological environment between in situ and ex situ individuals.
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Affiliation(s)
| | - Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.,Chubu University, Academy of Emerging Sciences, Kasugai 487-8501, Japan
| | | | | | - Atsushi Ueda
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | | | - Koichi Murata
- Faculty of Bioresource Sciences, Nihon University, Kanagawa 252-0800, Japan
| | - Hiroshi Nakamura
- General Foundation Hiroshi Nakamura International Institute for Ornithology, Nagano 380-0934, Japan
| | - Kazunari Ushida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.,Chubu University, Academy of Emerging Sciences, Kasugai 487-8501, Japan
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18
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Chen T, Li Y, Liang J, Li Y, Huang Z. Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China. Microbiologyopen 2020; 9:e981. [PMID: 31880067 PMCID: PMC7066464 DOI: 10.1002/mbo3.981] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota plays an important role in animal health and is strongly affected by the environment. Captivity and human source food have been shown to influence drastically the gut microbiota composition and function of wild animals. Therefore, in the present study, the gut microbiota of provisioned and wild populations of limestone-living rhesus macaques (Macaca mulatta) were compared using high-throughput 16S rRNA sequencing and bioinformatic analyses. The results indicated that provisioned macaques had a higher microbial richness than wild macaques, but there was no significant difference in the evenness of the gut microbiota between the two populations. Provisioned macaques also showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than wild macaques. Functional analysis revealed that wild macaques had enriched microbial pathways involved in glycan biosynthesis and metabolism, transport and catabolism, and the digestive and endocrine systems, while provisioned macaques were richer in pathways associated with signaling molecules and interaction, neurodegenerative diseases. These differences were likely due to modification of the gut microbiota of the provisioned macaques to enable the digestion of new foods.
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Affiliation(s)
- Ting Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Jipeng Liang
- Administration of Guangxi Chongzuo White‐headed Langur National Nature ReserveChongzuoChina
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
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19
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Frankel JS, Mallott EK, Hopper LM, Ross SR, Amato KR. The effect of captivity on the primate gut microbiome varies with host dietary niche. Am J Primatol 2019; 81:e23061. [PMID: 31713260 DOI: 10.1002/ajp.23061] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 09/13/2019] [Indexed: 01/01/2023]
Abstract
Despite careful attention to animal nutrition and wellbeing, gastrointestinal distress remains relatively common in captive non-human primates (NHPs), particularly dietary specialists such as folivores. These patterns may be a result of marked dietary differences between captive and wild settings and associated impacts on the gut microbiome. However, given that most existing studies target NHP dietary specialists, it is unclear if captive environments have distinct impacts on the gut microbiome of NHPs with different dietary niches. To begin to examine this question, we used 16S ribosomal RNA gene amplicon sequences to compare the gut microbiomes of five NHP genera categorized either as folivores (Alouatta, Colobus) or non-folivores (Cercopithecus, Gorilla, Pan) sampled both in captivity and in the wild. Though captivity affected the gut microbiomes of all NHPs in this study, the effects were largest in folivorous NHPs. Shifts in gut microbial diversity and in the relative abundances of fiber-degrading microbial taxa suggest that these findings are driven by marked dietary shifts for folivorous NHPs in captive settings. We propose that zoos and other captive care institutions consider including more natural browse in folivorous NHP diets and regularly bank fecal samples to further explore the relationship between NHP diet, the gut microbiome, and health outcomes.
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Affiliation(s)
- Jeffrey S Frankel
- Department of Anthropology, Northwestern University, Evanston, Illinois
| | | | - Lydia M Hopper
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois
| | - Stephen R Ross
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois
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20
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Shinohara A, Nohara M, Kondo Y, Jogahara T, Nagura-Kato GA, Izawa M, Koshimoto C. Comparison of the gut microbiotas of laboratory and wild Asian house shrews (Suncus murinus) based on cloned 16S rRNA sequences. Exp Anim 2019; 68:531-539. [PMID: 31217361 PMCID: PMC6842809 DOI: 10.1538/expanim.19-0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Asian house shrew, Suncus murinus, is an insectivore (Eulipotyphla,
Mammalia) and an important laboratory animal for life-science studies. The
gastrointestinal tract of Suncus is simple: the length of the entire
intestine is very short relative to body size, the large intestine is quite short, and
there are no fermentative chambers such as the forestomach or cecum. These features imply
that Suncus has a different nutritional physiology from those of humans
and mice, but little is known about whether Suncus utilizes microbial
fermentation in the large (LI) or small (SI) intestine. In addition, domestication may
affect the gastrointestinal microbial diversity of Suncus. Therefore, we
compared the gastrointestinal microbial diversity of Suncus between
laboratory and wild Suncus and between the SI and LI
(i.e., four groups: Lab-LI, Lab-SI, Wild-LI, and Wild-SI) using
bacterial 16S rRNA gene library sequencing analyses with a sub-cloning method. We obtained
759 cloned sequences (176, 174, 195, and 214 from the Lab-LI, Lab-SI, Wild-LI, and Wild-SI
samples, respectively), which revealed that the gastrointestinal microbiota of
Suncus is rich in Firmicutes (mostly lactic acid bacteria), with few
Bacteroidetes. We observed different bacterial communities according to intestinal region
in laboratory Suncus, but not in wild Suncus.
Furthermore, the gastrointestinal microbial diversity estimates were lower in laboratory
Suncus than in wild Suncus. These results imply that
Suncus uses lactic acid fermentation in the gut, and that the
domestication process altered the gastrointestinal bacterial diversity.
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Affiliation(s)
- Akio Shinohara
- Division of Bio-resources, Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Nohara
- Division of Bio-resources, Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.,Present Address: WDB EUREKA Co., Ltd., 2-3-2 Marunouchi, Chiyoda-ku, Tokyo, Japan
| | - Yuta Kondo
- Division of Bio-resources, Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takamichi Jogahara
- Division of Bio-resources, Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.,Present Address: Faculty of Law and Economics, Okinawa University, 555 Kokuba, Naha, Okinawa 902-8521, Japan
| | - Goro A Nagura-Kato
- Division of Bio-resources, Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Masako Izawa
- Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Chihiro Koshimoto
- Division of Bio-resources, Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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21
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Cryan JF, O'Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E, O'Connor R, Cruz-Pereira JS, Peterson VL, Rea K, Ritz NL, Sherwin E, Spichak S, Teichman EM, van de Wouw M, Ventura-Silva AP, Wallace-Fitzsimons SE, Hyland N, Clarke G, Dinan TG. The Microbiota-Gut-Brain Axis. Physiol Rev 2019; 99:1877-2013. [DOI: 10.1152/physrev.00018.2018] [Citation(s) in RCA: 1243] [Impact Index Per Article: 248.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within and on our bodies) as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis. This axis is gaining ever more traction in fields investigating the biological and physiological basis of psychiatric, neurodevelopmental, age-related, and neurodegenerative disorders. The microbiota and the brain communicate with each other via various routes including the immune system, tryptophan metabolism, the vagus nerve and the enteric nervous system, involving microbial metabolites such as short-chain fatty acids, branched chain amino acids, and peptidoglycans. Many factors can influence microbiota composition in early life, including infection, mode of birth delivery, use of antibiotic medications, the nature of nutritional provision, environmental stressors, and host genetics. At the other extreme of life, microbial diversity diminishes with aging. Stress, in particular, can significantly impact the microbiota-gut-brain axis at all stages of life. Much recent work has implicated the gut microbiota in many conditions including autism, anxiety, obesity, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. Animal models have been paramount in linking the regulation of fundamental neural processes, such as neurogenesis and myelination, to microbiome activation of microglia. Moreover, translational human studies are ongoing and will greatly enhance the field. Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strategies for neuropsychiatric disorders.
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Affiliation(s)
- John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kenneth J. O'Riordan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Caitlin S. M. Cowan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kiran V. Sandhu
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Thomaz F. S. Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Marcus Boehme
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Martin G. Codagnone
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Sofia Cussotto
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Christine Fulling
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Anna V. Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Katherine E. Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Minal Jaggar
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Caitriona M. Long-Smith
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Joshua M. Lyte
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Jason A. Martin
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Alicia Molinero-Perez
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Gerard Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Emanuela Morelli
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Enrique Morillas
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Rory O'Connor
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Joana S. Cruz-Pereira
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Veronica L. Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kieran Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Simon Spichak
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Emily M. Teichman
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Ana Paula Ventura-Silva
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Shauna E. Wallace-Fitzsimons
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Niall Hyland
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
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22
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Gibson KM, Nguyen BN, Neumann LM, Miller M, Buss P, Daniels S, Ahn MJ, Crandall KA, Pukazhenthi B. Gut microbiome differences between wild and captive black rhinoceros - implications for rhino health. Sci Rep 2019; 9:7570. [PMID: 31138833 PMCID: PMC6538756 DOI: 10.1038/s41598-019-43875-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
A number of recent studies have shown the importance of the mammalian gut microbiome in host health. In the context of endangered species, a few studies have examined the relationship between the gut microbiome in wild versus captive populations due to digestive and other health issues. Unfortunately, the results seem to vary across taxa in terms of captive animals having higher, lower, or equivalent microbiome diversity relative to their wild counterparts. Here, we focus on the black rhinoceros as captive animals suffer from a number of potentially dietary related health effects. We compared gut microbiomes of wild and captive black rhinos to test for differences in taxonomic diversity (alpha and beta) and in functional diversity of the microbiome. We incorporated a more powerful metagenomic shotgun sequencing approach rather than a targeted amplification of the 16S gene for taxonomic assignment of the microbiome. Our results showed no significant differences in the alpha diversity levels between wild and captive black rhinos, but significant differences in beta diversity. We found that bacterial taxa traditionally associated with ruminant guts of domesticated animals had higher relative abundances in captive rhinos. Our metagenomic sequencing results suggest that unknown gut microbes of wild rhinos are being replaced by those found in conventional human-domesticated livestock. Wild rhinos have significantly different functional bacterial communities compared to their captive counterparts. Functional profiling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients. Given the differences observed between wild and captive rhino gut microbiomes, we make a number of recommendations for potentially modifying captive gut microbiome to better reflect their wild counterparts and thereby hopefully improve overall rhino health in captivity.
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Affiliation(s)
- Keylie M Gibson
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Bryan N Nguyen
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Laura M Neumann
- Department of Environmental and Occupational Health, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Michele Miller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Peter Buss
- South African National Parks, Veterinary Wildlife Services, Kruger National Park, Skukuza, South Africa
| | - Savel Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, 7602, Matieland, South Africa
| | - Michelle J Ahn
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
- Department of Epidemiology and Biostatistics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Budhan Pukazhenthi
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
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23
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Hale VL, Tan CL, Niu K, Yang Y, Zhang Q, Knight R, Amato KR. Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi. Am J Primatol 2019; 81:e22989. [PMID: 31106872 DOI: 10.1002/ajp.22989] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/14/2019] [Accepted: 04/21/2019] [Indexed: 12/30/2022]
Abstract
Many colobine species-including the endangered Guizhou snub-nosed monkey (Rhinopithecus brelichi) are difficult to maintain in captivity and frequently exhibit gastrointestinal (GI) problems. GI problems are commonly linked to alterations in the gut microbiota, which lead us to examine the gut microbial communities of wild and captive R. brelichi. We used high-throughput sequencing of the 16S rRNA gene to compare the gut microbiota of wild (N = 7) and captive (N = 8) R. brelichi. Wild monkeys exhibited increased gut microbial diversity based on the Chao1 but not Shannon diversity metric and greater relative abundances of bacteria in the Lachnospiraceae and Ruminococcaceae families. Microbes in these families digest complex plant materials and produce butyrate, a short chain fatty acid critical to colonocyte health. Captive monkeys had greater relative abundances of Prevotella and Bacteroides species, which degrade simple sugars and carbohydrates, like those present in fruits and cornmeal, two staples of the captive R. brelichi diet. Captive monkeys also had a greater abundance of Akkermansia species, a microbe that can thrive in the face of host malnutrition. Taken together, these findings suggest that poor health in captive R. brelichi may be linked to diet and an altered gut microbiota.
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Affiliation(s)
- Vanessa L Hale
- Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Chia L Tan
- LVDI International, San Marcos, California.,Nonhuman Primate Conservation and Research Institute, Tongren University, Tongren, Guizhou, China
| | - Kefeng Niu
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Yeqin Yang
- Nonhuman Primate Conservation and Research Institute, Tongren University, Tongren, Guizhou, China
| | - Qikun Zhang
- Hangzhou KaiTai Biotechnology Co., Ltd, Hangzhou, China
| | - Rob Knight
- Pediatrics, University of California San Diego, La Jolla, California.,Computer Science and Engineering, University of California San Diego, La Jolla, California
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24
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Schmidt E, Mykytczuk N, Schulte-Hostedde AI. Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus). THE ISME JOURNAL 2019; 13:1293-1305. [PMID: 30664674 PMCID: PMC6474230 DOI: 10.1038/s41396-019-0345-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/09/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023]
Abstract
Vertebrate gastrointestinal tracts have co-existed with microbes over millennia. These microbial communities provide their host with numerous benefits. However, the extent to which different environmental factors contribute to the assemblage of gut microbial communities is not fully understood. The purpose of this study was to determine how the external environment influences the development of gut microbiome communities (GMCs). Faecal samples were collected from deer mice (Peromyscus maniculatus) born and raised in captivity and the wild at approximately 3-5 weeks of age. Additional samples were collected 2 weeks later, with a subset of individuals being translocated between captive and wild environments. Microbial data were analysed using 16S rRNA next-generation Illumina HiSeq sequencing methods. GMCs of deer mice were more similar between neighbours who shared the same environment, regardless of where an individual was born, demonstrating that GMCs are significantly influenced by the surrounding environment and can rapidly change over time. Mice in natural environments contained more diverse GMCs with higher relative abundances of Ruminoccocaceae, Helicobacteraceae and Lachnospiraceae spp. Future studies should examine the fitness consequences associated with the presence/absence of microbes that are characteristic of GMCs of wild populations to gain a better understanding of environment-microbe-host evolutionary and ecological relationships.
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Affiliation(s)
- Elliott Schmidt
- Department of Biology, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
| | - Nadia Mykytczuk
- Vale Living with Lakes Centre, Laurentian University, Sudbury, ON, P3E 2C6, Canada
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25
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Segawa T, Fukuchi S, Bodington D, Tsuchida S, Mbehang Nguema PP, Mori H, Ushida K. Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior. Microorganisms 2019; 7:microorganisms7040099. [PMID: 30987363 PMCID: PMC6518056 DOI: 10.3390/microorganisms7040099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/18/2023] Open
Abstract
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan.
| | - Dylan Bodington
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
| | | | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
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26
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Liu H, Chen Z, Gao G, Sun C, Li Y, Zhu Y. Characterization and comparison of gut microbiomes in nine species of parrots in captivity. Symbiosis 2019. [DOI: 10.1007/s13199-019-00613-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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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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28
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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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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.
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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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A comparative analysis of preservation techniques for the optimal molecular detection of hookworm DNA in a human fecal specimen. PLoS Negl Trop Dis 2018; 12:e0006130. [PMID: 29346412 PMCID: PMC5773002 DOI: 10.1371/journal.pntd.0006130] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/22/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time. METHODOLOGY Quantitative real-time PCR was used in this study as a measure of the effectiveness of seven commercially available products to preserve hookworm DNA over time and at different temperatures. Results were compared against "no preservative" controls and the "gold standard" of rapidly freezing samples at -20°C. The preservation methods were compared at both 4°C and at simulated tropical ambient temperature (32°C) over a period of 60 days. Evaluation of the effectiveness of each preservative was based on quantitative real-time PCR detection of target hookworm DNA. CONCLUSIONS At 4°C there were no significant differences in DNA amplification efficiency (as measured by Cq values) regardless of the preservation method utilized over the 60-day period. At 32°C, preservation with FTA cards, potassium dichromate, and a silica bead two-step desiccation process proved most advantageous for minimizing Cq value increases, while RNA later, 95% ethanol and Paxgene also demonstrate some protective effect. These results suggest that fecal samples spiked with known concentrations of hookworm-derived egg material can remain at 4°C for 60 days in the absence of preservative, without significant degradation of the DNA target. Likewise, a variety of preservation methods can provide a measure of protection in the absence of a cold chain. As a result, other factors, such as preservative toxicity, inhibitor resistance, preservative cost, shipping requirements, sample infectivity, and labor costs should be considered when deciding upon an appropriate method for the storage of fecal specimens for subsequent PCR analysis. Balancing logistical factors and the need to preserve the target DNA, we believe that under most circumstances 95% ethanol provides the most pragmatic choice for preserving stool samples in the field.
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Abstract
The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.
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Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
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32
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Nomoto R, Takano S, Tanaka K, Tsujikawa Y, Kusunoki H, Osawa R. Isolation and identification of Bifidobacterium species from feces of captive chimpanzees. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2017; 36:91-99. [PMID: 28748130 PMCID: PMC5510154 DOI: 10.12938/bmfh.16-027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022]
Abstract
Recently, gut-dwelling bifidobacteria from chimpanzees, which are phylogenetically close to humans and have feeding habits similar to humans, have been frequently investigated. Given this, we speculated that like humans,
chimpanzees would have a unique diversity of bifidobacteria. We herein describe a taxonomically novel member of bifidobacteria isolated from fecal samples of captive chimpanzees. Bifidobacteria were detected in all fecal samples
by quantitative polymerase chain reaction. A Bifidobacterium pseudolongum-like species, which could not be detected using B. pseudolongum-specific primers targeting the groEL gene
sequence, was dominant in the feces of five chimpanzees. Seven bifidobacterial strains were isolated from this group of five chimpanzees, and all isolates were identified as B. pseudolongum. B.
pseudolongum has previously often been isolated from non-primate animals as well as humans; however, here we demonstrate its presence in a nonhuman primate species.
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Affiliation(s)
- Ryohei Nomoto
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan.,Health Bioscience Team, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Shintaro Takano
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Kosei Tanaka
- Health Bioscience Team, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Yuji Tsujikawa
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Hiroshi Kusunoki
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
| | - Ro Osawa
- Department of Bioresource Science, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan.,Health Bioscience Team, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe 657-8501, Japan
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33
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Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Caviedes-Vidal E, Bordenstein SR. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol 2016; 26:1175-1189. [PMID: 27862531 DOI: 10.1111/mec.13921] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022]
Abstract
Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Antonio Brun
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Melisa Magallanes
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Joshua Brinkerhoff
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Alejandro Laspiur
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Juan Carlos Acosta
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Enrique Caviedes-Vidal
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA
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34
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Effects of field conditions on fecal microbiota. J Microbiol Methods 2016; 130:180-188. [DOI: 10.1016/j.mimet.2016.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 02/08/2023]
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35
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Su C, Zuo R, Liu W, Sun Y, Li Z, Jin X, Jia K, Yang Y, Zhang H. Fecal Bacterial Composition of Sichuan Snub-Nosed Monkeys (Rhinopithecus roxellana). INT J PRIMATOL 2016. [DOI: 10.1007/s10764-016-9918-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Abstract
The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.
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37
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The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems 2016; 1:mSystems00046-16. [PMID: 27822543 PMCID: PMC5069958 DOI: 10.1128/msystems.00046-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/06/2016] [Indexed: 02/01/2023] Open
Abstract
Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.
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Kohl KD, Dearing MD. The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins. Front Microbiol 2016; 7:1165. [PMID: 27516760 PMCID: PMC4963388 DOI: 10.3389/fmicb.2016.01165] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/13/2016] [Indexed: 01/22/2023] Open
Abstract
The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma) that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, non-gastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host's ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that could be useful in the treatment of diseases in humans and domestic animals.
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Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences, Vanderbilt University, NashvilleTN, USA
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Hale VL, Tan CL, Knight R, Amato KR. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods 2015; 113:16-26. [PMID: 25819008 DOI: 10.1016/j.mimet.2015.03.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/24/2015] [Accepted: 03/24/2015] [Indexed: 02/07/2023]
Abstract
Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis.
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Affiliation(s)
- Vanessa L Hale
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA.
| | - Chia L Tan
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California San Diego, La Jolla, California 92093, USA.
| | - Katherine R Amato
- Department of Anthropology, University of Colorado, Boulder, CO 80309, USA.
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Mbehang Nguema PP, Tsuchida S, Ushida K. Bacteria culturing and isolation under field conditions of Moukalaba-Doudou National Park, Gabon, and preliminary survey on bacteria carrying antibiotic resistance genes. TROPICS 2015. [DOI: 10.3759/tropics.23.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
| | - Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
| | - Kazunari Ushida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
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41
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Tsuchida S, Ushida K. Characterization of intestinal bacterial communities of western lowland gorillas ( Gorilla gorilla gorilla), central chimpanzees ( Pan troglodytes troglodytes), and a forest elephant ( Loxodonta africana cyclotis) living in Moukalaba-Doudou National Park in Gabon. TROPICS 2015. [DOI: 10.3759/tropics.23.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
| | - Kazunari Ushida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
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42
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Kohl KD, Dearing MD. Wild-caught rodents retain a majority of their natural gut microbiota upon entrance into captivity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:191-5. [PMID: 24596293 DOI: 10.1111/1758-2229.12118] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/22/2013] [Indexed: 05/20/2023]
Abstract
Experiments conducted on captive animals allow scientists to control many variables; however, these settings are highly unnatural. Previous research has documented a large difference in microbial communities between wild animals and captive-bred individuals. However, wild-caught animals brought into captivity might retain their natural microbiota and thus provide a better study system in which to investigate the ecology of the gut microbiome. We collected individuals of the desert woodrat (Neotoma lepida) from nature and investigated changes in the microbial community over 6 months in captivity. Additionally, we inventoried potential environmental sources of microbes (food, bedding) from the wild and captivity. We found that environmental sources do not make large contributions to the woodrat gut microbial community. We documented a slight decrease in several biodiversity metrics over 6 months in captivity, yet the magnitude of change was small compared with other studies. Wild and captive animals shared 64% of their microbial species, almost twice that observed in other studies of wild and captive-bred individuals (≤ 37% shared). We conclude that wild-caught animals brought into captivity retain a substantial proportion of their natural microbiota and represent an acceptable system in which to study the gut microbiome.
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Affiliation(s)
- Kevin D Kohl
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
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McCord AI, Chapman CA, Weny G, Tumukunde A, Hyeroba D, Klotz K, Koblings AS, Mbora DNM, Cregger M, White BA, Leigh SR, Goldberg TL. Fecal microbiomes of non-human primates in Western Uganda reveal species-specific communities largely resistant to habitat perturbation. Am J Primatol 2013; 76:347-54. [PMID: 24285224 DOI: 10.1002/ajp.22238] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/16/2013] [Accepted: 10/27/2013] [Indexed: 01/15/2023]
Abstract
Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate "microbiomes" remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance.
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Affiliation(s)
- Aleia I McCord
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, Wisconsin
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Tsuchida S, Takahashi S, Nguema PPM, Fujita S, Kitahara M, Yamagiwa J, Ngomanda A, Ohkuma M, Ushida K. Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla). Int J Syst Evol Microbiol 2013; 64:449-455. [PMID: 24158945 DOI: 10.1099/ijs.0.055186-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-staining-positive anaerobic rods were isolated from the faeces of a wild lowland gorilla (Gorilla gorilla gorilla) in Moukalaba-Doudou National Park, Gabon, and strain GG01(T) was taxonomically investigated. Based on phylogenetic analyses and specific phenotypic characteristics, the strain belonged to the genus Bifidobacterium. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain GG01(T) formed a single monophyletic cluster and had a distinct line of descent. Based on 16S rRNA gene sequence similarity, the type strains of Bifidobacterium catenulatum JCM 1194(T) (98.3%) and Bifidobacterium pseudocatenulatum (98.1%) JCM 1200(T) were the most closely related to this novel strain, although it was clear that they belonged to different species. hsp60 sequences also supported these relationships. The DNA G+C content of this novel strain was 60.1 mol%. Bifidobacterium moukalabense sp. nov. (type strain GG01(T) = JCM 18751(T) = DSM 27321(T)) is proposed.
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Affiliation(s)
- Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
| | | | | | - Shiho Fujita
- Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Juichi Yamagiwa
- Graduate School of Science, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Alfred Ngomanda
- Research Institute of Tropical Ecology, Libreville, Bp 13354, Gabon
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kazunari Ushida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
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Drakulovski P, Locatelli S, Butel C, Pion S, Krasteva D, Mougdi-Pole E, Delaporte E, Peeters M, Mallié M. Use of RNAlater as a preservation method for parasitic coprology studies in wild-living chimpanzees. Exp Parasitol 2013; 135:257-61. [PMID: 23850999 DOI: 10.1016/j.exppara.2013.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 11/20/2022]
Abstract
We evaluated the use of an RNA stabilisation buffer, RNAlater (Ambion, Austin, Texas), as a preservation medium for parasitic coprology analysis of faecal samples collected from chimpanzees living in the wild (Pan troglodytes troglodytes). Thirty faecal samples collected in the forests of south-east Cameroon (Mambele area) from 2003 to 2011 were preserved in RNAlater at -80 °C and analysed for their parasite content. We identified and counted parasitic elements and assessed their shape, size and morphology in relation to the storage time of the samples. We found that parasite elements were identifiable in RNAlater preserved samples after as many as 7 years, showing that RNAlater could be an effective and reliable preservation medium for coprology. Thus, its use could be an interesting way to optimise sample collection for several types of studies (parasitology and bacteriology/virology) at once, especially considering the logistically challenging and time-consuming field campaigns needed to obtain these faecal samples.
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Affiliation(s)
- P Drakulovski
- UMI 233 "TransVIHMI", Institut de Recherche pour le Developpement (IRD), University of Montpellier 1 (UM1), Montpellier, France.
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Xu B, Xu W, Yang F, Li J, Yang Y, Tang X, Mu Y, Zhou J, Huang Z. Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds. PLoS One 2013; 8:e56565. [PMID: 23457582 PMCID: PMC3574064 DOI: 10.1371/journal.pone.0056565] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 01/11/2013] [Indexed: 01/29/2023] Open
Abstract
The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. An analysis of 78,619 pyrosequencing reads generated from pygmy loris fecal DNA extracts was performed to help better understand the microbial diversity and functional capacity of the pygmy loris gut microbiome. The taxonomic analysis of the metagenomic reads indicated that pygmy loris fecal microbiomes were dominated by Bacteroidetes and Proteobacteria phyla. The hierarchical clustering of several gastrointestinal metagenomes demonstrated the similarities of the microbial community structures of pygmy loris and mouse gut systems despite their differences in functional capacity. The comparative analysis of function classification revealed that the metagenome of the pygmy loris was characterized by an overrepresentation of those sequences involved in aromatic compound metabolism compared with humans and other animals. The key enzymes related to the benzoate degradation pathway were identified based on the Kyoto Encyclopedia of Genes and Genomes pathway assignment. These results would contribute to the limited body of primate metagenome studies and provide a framework for comparative metagenomic analysis between human and non-human primates, as well as a comparative understanding of the evolution of humans and their microbiome. However, future studies on the metagenome sequencing of pygmy loris and other prosimians regarding the effects of age, genetics, and environment on the composition and activity of the metagenomes are required.
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Affiliation(s)
- Bo Xu
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Weijiang Xu
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Fuya Yang
- School of Life Science, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Junjun Li
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Yunjuan Yang
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Xianghua Tang
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Yuelin Mu
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Junpei Zhou
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
- * E-mail:
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Nelson TM, Rogers TL, Carlini AR, Brown MV. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ Microbiol 2012; 15:1132-45. [PMID: 23145888 DOI: 10.1111/1462-2920.12022] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/27/2012] [Accepted: 10/08/2012] [Indexed: 02/03/2023]
Abstract
The gut microbiota of mammals underpins the metabolic capacity and health of the host. Our understanding of what influences the composition of this community has been limited primarily to evidence from captive and terrestrial mammals. Therefore, the gut microbiota of southern elephant seals, Mirounga leonina, and leopard seals, Hydrurga leptonyx, inhabiting Antarctica were compared with captive leopard seals. Each seal exhibited a gut microbiota dominated by four phyla: Firmicutes (41.5 ± 4.0%), Fusobacteria (25.6 ± 3.9%), Proteobacteria (17.0 ± 3.2%) and Bacteroidetes (14.1 ± 1.7%). Species, age, sex and captivity were strong drivers of the composition of the gut microbiota, which can be attributed to differences in diet, gut length and physiology and social interactions. Differences in particular prey items consumed by seal species could contribute to the observed differences in the gut microbiota. The longer gut of the southern elephant seal provides a habitat reduced in available oxygen and more suitable to members of the phyla Bacteroidetes compared with other hosts. Among wild seals, 16 'core' bacterial community members were present in the gut of at least 50% of individuals. As identified between southern elephant seal mother-pup pairs, 'core' members are passed on via vertical transmission from a young age and persist through to adulthood. Our study suggests that these hosts have co-evolved with their gut microbiota and core members may provide some benefit to the host, such as developing the immune system. Further evidence of their strong evolutionary history is provided with the presence of 18 shared 'core' members in the gut microbiota of related seals living in the Arctic. The influence of diet and other factors, particularly in captivity, influences the composition of the community considerably. This study suggests that the gut microbiota has co-evolved with wild mammals as is evident in the shared presence of 'core' members.
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Affiliation(s)
- Tiffanie M Nelson
- Evolution and Ecology Research Centre, University of New South Wales, Kensington, New South Wales, Australia.
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Vlčková K, Mrázek J, Kopečný J, Petrželková KJ. Evaluation of different storage methods to characterize the fecal bacterial communities of captive western lowland gorillas (Gorilla gorilla gorilla). J Microbiol Methods 2012; 91:45-51. [DOI: 10.1016/j.mimet.2012.07.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 12/18/2022]
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Bengmark S. Gut microbiota, immune development and function. Pharmacol Res 2012; 69:87-113. [PMID: 22989504 DOI: 10.1016/j.phrs.2012.09.002] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/01/2012] [Indexed: 02/08/2023]
Abstract
The microbiota of Westerners is significantly reduced in comparison to rural individuals living a similar lifestyle to our Paleolithic forefathers but also to that of other free-living primates such as the chimpanzee. The great majority of ingredients in the industrially produced foods consumed in the West are absorbed in the upper part of small intestine and thus of limited benefit to the microbiota. Lack of proper nutrition for microbiota is a major factor under-pinning dysfunctional microbiota, dysbiosis, chronically elevated inflammation, and the production and leakage of endotoxins through the various tissue barriers. Furthermore, the over-comsumption of insulinogenic foods and proteotoxins, such as advanced glycation and lipoxidation molecules, gluten and zein, and a reduced intake of fruit and vegetables, are key factors behind the commonly observed elevated inflammation and the endemic of obesity and chronic diseases, factors which are also likely to be detrimental to microbiota. As a consequence of this lifestyle and the associated eating habits, most barriers, including the gut, the airways, the skin, the oral cavity, the vagina, the placenta, the blood-brain barrier, etc., are increasingly permeable. Attempts to recondition these barriers through the use of so called 'probiotics', normally applied to the gut, are rarely successful, and sometimes fail, as they are usually applied as adjunctive treatments, e.g. in parallel with heavy pharmaceutical treatment, not rarely consisting in antibiotics and chemotherapy. It is increasingly observed that the majority of pharmaceutical drugs, even those believed to have minimal adverse effects, such as proton pump inhibitors and anti-hypertensives, in fact adversely affect immune development and functions and are most likely also deleterious to microbiota. Equally, it appears that probiotic treatment is not compatible with pharmacological treatments. Eco-biological treatments, with plant-derived substances, or phytochemicals, e.g. curcumin and resveratrol, and pre-, pro- and syn-biotics offers similar effects as use of biologicals, although milder but also free from adverse effects. Such treatments should be tried as alternative therapies; mainly, to begin with, for disease prevention but also in early cases of chronic diseases. Pharmaceutical treatment has, thus far, failed to inhibit the tsunami of endemic diseases spreading around the world, and no new tools are in sight. Dramatic alterations, in direction of a paleolithic-like lifestyle and food habits, seem to be the only alternatives with the potential to control the present escalating crisis. The present review focuses on human studies, especially those of clinical relevance.
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Affiliation(s)
- Stig Bengmark
- Division of Surgery & Interventional Science, University College London, 4th floor, 74 Huntley Street, London WC1E 6AU, United Kingdom.
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50
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Nakamura N, Amato KR, Garber P, Estrada A, Mackie RI, Gaskins HR. Analysis of the hydrogenotrophic microbiota of wild and captive black howler monkeys (Alouatta pigra) in palenque national park, Mexico. Am J Primatol 2011; 73:909-19. [DOI: 10.1002/ajp.20961] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 04/01/2011] [Accepted: 04/07/2011] [Indexed: 11/12/2022]
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