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Greene LK, McKenney EA, Gasper W, Wrampelmeier C, Hayer S, Ehmke EE, Clayton JB. Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs. MICROBIAL ECOLOGY 2023; 85:1608-1619. [PMID: 35562600 DOI: 10.1007/s00248-022-02034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/05/2022] [Indexed: 05/10/2023]
Abstract
Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.
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Affiliation(s)
- Lydia K Greene
- The Duke Lemur Center, Duke University, Durham, NC, 27705, USA.
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA
| | - William Gasper
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Claudia Wrampelmeier
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Shivdeep Hayer
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Erin E Ehmke
- The Duke Lemur Center, Duke University, Durham, NC, 27705, USA
| | - Jonathan B Clayton
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Zeng Y, Pu Y, Niu L, Deng J, Zeng D, Amato K, Li Y, Zhou Y, Lin Y, Wang J, Wu L, Chen B, Pan K, Jing B, Ni X. Comparison of gastrointestinal microbiota in golden snub-nosed monkey (Rhinopithecus roxellanae), green monkey (Chlorocebus aethiops sabaeus), and ring-tailed lemur (Lemur catta) by high throughput sequencing. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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