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Zhang Z, Bao C, Li Z, He C, Jin W, Li C, Chen Y. Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis. Appl Microbiol Biotechnol 2024; 108:125. [PMID: 38229330 DOI: 10.1007/s00253-023-12841-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 01/18/2024]
Abstract
The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.
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Affiliation(s)
- Zhenxiang Zhang
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Changhong Bao
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Zhaonan Li
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Caixia He
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Wenjie Jin
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Changzhong Li
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
| | - Yanxia Chen
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
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Li S, Mu R, Zhu Y, Zhao F, Qiu Q, Si H, Wright ADG, Li Z. Shifts in the microbial community and metabolome in rumen ecological niches during antler growth. Comput Struct Biotechnol J 2024; 23:1608-1618. [PMID: 38680874 PMCID: PMC11047195 DOI: 10.1016/j.csbj.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/29/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.
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Affiliation(s)
- Songze Li
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Ruina Mu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yuhang Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Fei Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710100, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Jilin Agricultural University, Changchun 130118, China
| | | | - Zhipeng Li
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Jilin Agricultural University, Changchun 130118, China
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Manus MB, Lucore J, Kuthyar S, Moy M, Savo Sardaro ML, Amato KR. Technical note: A biological anthropologist's guide for applying microbiome science to studies of human and non-human primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e25020. [PMID: 39222382 DOI: 10.1002/ajpa.25020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/28/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
A central goal of biological anthropology is connecting environmental variation to differences in host physiology, biology, health, and evolution. The microbiome represents a valuable pathway for studying how variation in host environments impacts health outcomes. While there are many resources for learning about methods related to microbiome sample collection, laboratory analyses, and genetic sequencing, there are fewer dedicated to helping researchers navigate the dense portfolio of bioinformatics and statistical approaches for analyzing microbiome data. Those that do exist are rarely related to questions in biological anthropology and instead are often focused on human biomedicine. To address this gap, we expand on existing tutorials and provide a "road map" to aid biological anthropologists in understanding, selecting, and deploying the data analysis and visualization methods that are most appropriate for their specific research questions. Leveraging an existing dataset of fecal samples and survey data collected from wild geladas living in Simien Mountains National Park in Ethiopia (Baniel et al., 2021), this paper guides researchers toward answering three questions related to variation in the gut microbiome across host and environmental factors. By providing explanations, examples, and a reproducible workflow for different analytic methods, we move beyond the theoretical benefits of considering the microbiome within anthropological research and instead present researchers with a guide for applying microbiome science to their work. This paper makes microbiome science more accessible to biological anthropologists and paves the way for continued research into the microbiome's role in the ecology, evolution, and health of human and non-human primates.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas, USA
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Jordan Lucore
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Madelyn Moy
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maria Luisa Savo Sardaro
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Human Science and Promotion of the Quality of Life, University of San Raffaele, Rome, Italy
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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Whitney TL, Mallott EK, Diakiw LO, Christie DM, Ting N, Amato KR, Tecot SR, Baden AL. Ecological and genetic variables co-vary with social group identity to shape the gut microbiome of a pair-living primate. Am J Primatol 2024; 86:e23657. [PMID: 38967215 DOI: 10.1002/ajp.23657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 05/17/2024] [Accepted: 06/08/2024] [Indexed: 07/06/2024]
Abstract
Primates exhibit diverse social systems that are intricately linked to their biology, behavior, and evolution, all of which influence the acquisition and maintenance of their gut microbiomes (GMs). However, most studies of wild primate populations focus on taxa with relatively large group sizes, and few consider pair-living species. To address this gap, we investigate how a primate's social system interacts with key environmental, social, and genetic variables to shape the GM in pair-living, red-bellied lemurs (Eulemur rubriventer). Previous research on this species suggests that social interactions within groups influence interindividual microbiome similarity; however, the impacts of other nonsocial variables and their relative contributions to gut microbial variation remain unclear. We sequenced the 16S ribosomal RNA hypervariable V4-V5 region to characterize the GM from 26 genotyped individuals across 11 social groups residing in Ranomafana National Park, Madagascar. We estimated the degree to which sex, social group identity, genetic relatedness, dietary diversity, and home range proximity were associated with variation in the gut microbial communities residing in red-bellied lemurs. All variables except sex played a significant role in predicting GM composition. Our model had high levels of variance inflation, inhibiting our ability to determine which variables were most predictive of gut microbial composition. This inflation is likely due to red-bellied lemurs' pair-living, pair-bonded social system that leads to covariation among environmental, social, and genetic variables. Our findings highlight some of the factors that predict GM composition in a tightly bonded, pair-living species and identify variables that require further study. We propose that future primate microbiome studies should simultaneously consider environmental, social, and genetic factors to improve our understanding of the relationships among sociality, the microbiome, and primate ecology and evolution.
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Affiliation(s)
- Tabor L Whitney
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Laura O Diakiw
- Department of Ecology, University of Wyoming, Laramie, Wyoming, USA
| | - Diana M Christie
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Stacey R Tecot
- School of Anthropology, University of Arizona, Tucson, Arizona, USA
| | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York City, New York, USA
- Department of Anthropology, The Graduate Center of the City University of New York, New York City, New York, USA
- The New York Consortium in Evolutionary Primatology, New York City, New York, USA
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Shang Z, Chen K, Han T, Bu F, Sun S, Zhu N, Man D, Yang K, Yuan S, Fu H. Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China. Animals (Basel) 2024; 14:2334. [PMID: 39199868 PMCID: PMC11350848 DOI: 10.3390/ani14162334] [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: 06/25/2024] [Revised: 07/30/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.
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Affiliation(s)
- Zhenghaoni Shang
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Kai Chen
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Tingting Han
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Fan Bu
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Shanshan Sun
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Na Zhu
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Duhu Man
- College of Agriculture, Hulunbuir University, Hulunbuir 021000, China;
| | - Ke Yang
- Alxa League Meteorological Bureau, Alxa 750300, China;
| | - Shuai Yuan
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
| | - Heping Fu
- College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.S.); (K.C.); (T.H.); (F.B.); (S.S.); (N.Z.)
- Key Laboratory of Grassland Rodent Ecology and Pest Controlled, Hohhot 010011, China
- Key Laboratory of Grassland Resources, Ministry of Education, Hohhot 010011, China
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Worsley SF, Davies CS, Lee CZ, Mannarelli ME, Burke T, Komdeur J, Dugdale HL, Richardson DS. Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population. Mol Ecol 2024; 33:e17477. [PMID: 39010794 DOI: 10.1111/mec.17477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 07/17/2024]
Abstract
In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (Acrocephalus sechellensis) to investigate how bacterial GM alpha diversity, composition and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Chuen Zhang Lee
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | | | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Nature Seychelles, Mahé, Republic of Seychelles
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Finnegan PM, Garber PA, McKenney AC, Bicca-Marques JC, De la Fuente MF, Abreu F, Souto A, Schiel N, Amato KR, Mallott EK. Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate. mSphere 2024; 9:e0023324. [PMID: 38940510 PMCID: PMC11288025 DOI: 10.1128/msphere.00233-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (Callithrix jacchus) exploiting a hot, dry environment-Caatinga-in northeastern Brazil. We collected fecal samples during two time periods (July-August and February-March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets' diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome. IMPORTANCE In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.
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Affiliation(s)
- Peter M. Finnegan
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Paul A. Garber
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Anna C. McKenney
- Department of Natural Sciences, Parkland College, Champaign, Illinois, USA
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católicado Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Filipa Abreu
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - Antonio Souto
- Department of Zoology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Nicola Schiel
- Laboratório de Etologia Teórica e Aplicada, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Katherine R. Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K. Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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8
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Yan W, Wang D, Wang Y, Wang C, Chen X, Liu L, Wang Y, Li YY, Kamagata Y, Nobu MK, Zhang T. Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities. MICROBIOME 2024; 12:121. [PMID: 38970122 PMCID: PMC11225162 DOI: 10.1186/s40168-024-01830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. RESULTS In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. CONCLUSION Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.
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Affiliation(s)
- Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masaru K Nobu
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao SAR, China.
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9
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Perlman RF, Beehner JC, Koenig A, Lu A. Consumption of underground storage organs is associated with improved energetic status in a graminivorous primate. J Hum Evol 2024; 192:103545. [PMID: 38843698 DOI: 10.1016/j.jhevol.2024.103545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 06/23/2024]
Abstract
Early hominin species likely had access to open, grassy habitats where periodic reliance on underground storage organs (USOs) is hypothesized to have played a crucial dietary role. As the only living graminivorous primate today, geladas (Theropithecus gelada) provide a unique perspective for understanding the energetic consequences of seasonal consumption of USOs. Geladas rely heavily on above-ground grasses throughout the year, but when grass is seasonally less available, they feed more on USOs. To assess whether USOs fit the definition of fallback foods (i.e., foods that are difficult to access, less preferred, or both), we examined how foraging effort (measured via time spent feeding and moving) and energetic status (measured via urinary C-peptide) fluctuated during seasonal dietary changes in a population of wild geladas in the Simien Mountains National Park, Ethiopia. If, indeed, USOs are fallback foods, we predicted an increase in foraging effort and a decline in energetic status during the dry season, when geladas rely more heavily on USOs. We collected behavioral and physiological data from 13 adult gelada males across a 13-month period. As expected, we found that male geladas spent more time moving during drier months. However, counter to the hypothesis that USOs are fallback foods in geladas, urinary C-peptide concentrations were significantly higher during the dry season. We suggest that USOs may represent an energy-rich food item for geladas, but it remains unclear why USOs are not consumed year-round. Future work is needed to better understand seasonal variation in the availability, nutrient content, and digestibility of USOs. However, results indicate that exploiting USOs seasonally could have been a valuable dietary strategy for the evolutionary success of early hominins.
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Affiliation(s)
- Rachel F Perlman
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794-4364, USA; Program for Research Initiatives in Science & Math, John Jay College of Criminal Justice, City University of New York, New York, NY 10019, USA.
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109-1043, USA; Department of Anthropology, University of Michigan, Ann Arbor, MI 48109-1107, USA
| | - Andreas Koenig
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794-4364, USA; Department of Anthropology, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | - Amy Lu
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794-4364, USA; Department of Anthropology, Stony Brook University, Stony Brook, NY 11794-4364, USA.
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10
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Wu Y, Deng N, Liu J, Cai Y, Yi X, Tan Z. Unlocking the therapeutic potential of Huoxiang Zhengqi San in cold and high humidity-induced diarrhea: Insights into intestinal microbiota modulation and digestive enzyme activity. Heliyon 2024; 10:e32789. [PMID: 38975065 PMCID: PMC11226830 DOI: 10.1016/j.heliyon.2024.e32789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
Huoxiang Zhengqi San (HXZQS), a traditional Chinese herbal formula, enjoys widespread use in Chinese medicine to treat diarrhea with cold-dampness trapped spleen syndrome (CDSS), which is induced by exposure to cold and high humidity stress. This study aimed to explore its therapeutic mechanisms in mice, particularly focusing on the intestinal microbiota. Forty male SPF-grade KM mice were allocated into two groups: the normal control group (H-Cc, n = 10) and the CDSS group (H-Mc, n = 30). After modeling, H-Mc was subdivided into H-Mc (n = 15) and HXZQS treatment (H-Tc, n = 15) groups. Intestinal samples were analyzed for enzyme activity and microbiota composition. Our findings demonstrated a notable reduction in intestinal lactase activity post-HXZQS treatment (P < 0.05). Lactobacillus johnsonii, Lactobacillus reuteri, and Lactobacillus murinus emerged as the main dominant species across most groups. However, in the H-Mc group, Clostridium sensu stricto 1 was identified as the exclusive dominant bacteria. LEfSe analysis highlighted Clostridiales vadinBB60 group and Corynebacterium as differential bacteria in the H-Tc group, and Cyanobacteria unidentified specie in the H-Mc group. Predicted microbiota functions aligned with changes in abundance, notably in cofactors and vitamins metabolism. The collinear results of the intestinal microbiota interaction network showed that HXZQS restored cooperative interactions among rare bacteria by mitigating their mutual promotion. The HXZQS decoction effectively alleviates diarrhea with CDSS by regulating intestinal microbiota, digestive enzyme activity, and microbiota interaction. Notably, it enhances Clostridium vadinBB60 and suppresses Cyanobacteria unidentified specie, warranting further study.
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Affiliation(s)
- Yi Wu
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Na Deng
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Jing Liu
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Ying Cai
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Xin Yi
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Zhoujin Tan
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
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11
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Guo Y, Garber PA, Yang Y, Wang S, Zhou J. The Conservation Implications of the Gut Microbiome for Protecting the Critically Endangered Gray Snub-Nosed Monkey ( Rhinopithecus brelichi). Animals (Basel) 2024; 14:1917. [PMID: 38998029 PMCID: PMC11240530 DOI: 10.3390/ani14131917] [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: 05/27/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
The gut microbiota plays a crucial role in regulating energy metabolism, facilitating nutrient absorption, and supporting immune function, thereby assisting the host in adapting to seasonal dietary changes. Here, we compare the gut microbiome composition of wild gray snub-nosed monkeys during winter (from October to December) and spring (from January to March) to understand differences in seasonal nutrient intake patterns. Snub-nosed monkeys are foregut fermenters and consume difficult-to-digest carbohydrates and lichen. To examine the digestive adaptations of gray snub-nosed monkeys, we collected 14 fresh fecal samples for DNA analysis during the winter and spring. Based on 16S rRNA sequencing, metagenomic sequencing, and functional metagenomic analyses, we identified that Firmicutes, Actinobacteria, Verrucomicrobia, and Bacteroidetes constitute a keystone bacterial group in the gut microbiota during winter and spring and are responsible for degrading cellulose. Moreover, the transition in dietary composition from winter to spring was accompanied by changes in gut microbiota composition, demonstrating adaptive responses to varying food sources and availability. In winter, the bacterial species of the genera Streptococcus were found in higher abundance. At the functional level, these bacteria are involved in fructose and mannose metabolism and galactose metabolism c-related pathways, which facilitate the breakdown of glycogen, starch, and fiber found in fruits, seeds, and mature leaves. During spring, there was an increased abundance of bacteria species from the Prevotella and Lactobacillus genera, which aid the digestion of protein-rich buds. Combined, these findings reveal how the gut microbiota adjusts to fluctuations in energy balance and nutrient intake across different seasons in this critically endangered species. Moreover, we also identified Pseudomonas in two samples; the presence of potential pathogens within the gut could pose a risk to other troop members. Our findings highlight the necessity of a conservation plan that focuses on protecting vegetation and implementing measures to prevent disease transmission for this critically endangered species.
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Affiliation(s)
- Yanqing Guo
- College of Life Sciences, Northwest University, Xi'an 710072, China
| | - Paul A Garber
- Program in Ecology, Evolution and Conservation Biology, Department of Anthropology, University of Illinois, Urbana, IL 61801, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali 671000, China
| | - Yijun Yang
- College of Life Sciences, Northwest University, Xi'an 710072, China
| | - Siwei Wang
- School of Karst Science, Guizhou Normal University, Guiyang 550003, China
| | - Jiang Zhou
- School of Karst Science, Guizhou Normal University, Guiyang 550003, China
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12
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Grieneisen L, Hays A, Cook E, Blekhman R, Tecot S. Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type. Am J Primatol 2024:e23656. [PMID: 38873762 DOI: 10.1002/ajp.23656] [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: 06/01/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, BC, Canada
| | - Allison Hays
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Erica Cook
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stacey Tecot
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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13
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Galià-Camps C, Junkin L, Borrallo X, Carreras C, Pascual M, Turon X. Navigating spatio-temporal microbiome dynamics: Environmental factors and trace elements shape the symbiont community of an invasive marine species. MARINE POLLUTION BULLETIN 2024; 203:116477. [PMID: 38759466 DOI: 10.1016/j.marpolbul.2024.116477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
The proliferation of marine invasive species is a mounting concern. While the role of microbial communities in invasive ascidian species is recognized, the role of seasonal shifts in microbiome composition remains largely unexplored. We sampled five individuals of the invasive ascidian Styela plicata quarterly from January 2020 to October 2021 in two harbours, examining gills, tunics, and surrounding water. By analysing Amplicon Sequence Variants (ASVs) and seawater trace elements, we found that compartment (seawater, tunic, or gills) was the primary differentiating factor, followed by harbour. Clear seasonal patterns were evident in seawater bacteria, less so in gills, and absent in tunics. We identified compartment-specific bacteria, as well as seasonal indicator ASVs and ASVs correlated with trace element concentrations. Among these bacteria, we found that Endozoicomonas, Hepatoplasma and Rhodobacteraceae species had reported functions which might be necessary for overcoming seasonality and trace element shifts. This study contributes to understanding microbiome dynamics in invasive holobiont systems, and the patterns found indicate a potential role in adaptation and invasiveness.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain; Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
| | - Liam Junkin
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.
| | - Xavier Borrallo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
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14
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Härer A, Frazier CJ, Rennison DJ. Host ecotype and rearing environment are the main drivers of threespine stickleback gut microbiota diversity in a naturalistic experiment. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240649. [PMID: 39100190 PMCID: PMC11296155 DOI: 10.1098/rsos.240649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/01/2024] [Indexed: 08/06/2024]
Abstract
Host-microbiota interactions play a critical role in the hosts' biology, and thus, it is crucial to elucidate the mechanisms that shape gut microbial communities. We leveraged threespine stickleback fish (Gasterosteus aculeatus) as a model system to investigate the contribution of host and environmental factors to gut microbiota variation. These fish offer a unique opportunity for experiments in naturalistic conditions; we reared benthic and limnetic ecotypes from three different lakes in experimental ponds, allowing us to assess the relative effects of shared environment (pond), geographic origin (lake-of-origin), trophic ecology and genetics (ecotype) and biological sex on gut microbiota α- and β-diversity. Host ecotype had the strongest influence on α-diversity, with benthic fish exhibiting higher diversity than limnetic fish, followed by the rearing environment. β-diversity was primarily shaped by rearing environment, followed by host ecotype, indicating that environmental factors play a crucial role in determining gut microbiota composition. Furthermore, numerous bacterial orders were differentially abundant across ponds, underlining the substantial contribution of environmental factors to gut microbiota variation. Our study illustrates the complex interplay between environmental and host ecological or genetic factors in shaping the stickleback gut microbiota and highlights the value of experiments conducted under naturalistic conditions for understanding gut microbiota dynamics.
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Affiliation(s)
- Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Christine J. Frazier
- School of Biological Sciences, Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Diana J. Rennison
- School of Biological Sciences, Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
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15
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Marsh KJ, Bearhop S, Harrison XA. Linking microbiome temporal dynamics to host ecology in the wild. Trends Microbiol 2024:S0966-842X(24)00132-X. [PMID: 38797653 DOI: 10.1016/j.tim.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024]
Abstract
Ignoring the dynamic nature of microbial communities risks underestimating the power of microbes to impact the health of their hosts. Microbiomes are thought to be important for host fitness, yet the coarse temporal scale and population-level focus of many studies precludes the ability to investigate the importance of among-individual variation in stability and identify the ecological contexts in which this variation matters. Here we briefly summarise current knowledge of temporal dynamics in wild host-associated microbial communities. We then discuss the implications of among-individual variation in microbiota stability and suggest analytical approaches for understanding these patterns. One major requirement is for future studies to conduct individual-level longitudinal analyses, with some systems already well set up for answering these questions.
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Affiliation(s)
- Kirsty J Marsh
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK.
| | - Stuart Bearhop
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK
| | - Xavier A Harrison
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK.
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16
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Zheng P, Gao W, Cong S, Leng L, Wang T, Shi L. High-Energy Supplemental Feeding Shifts Gut Microbiota Composition and Function in Red Deer ( Cervus elaphus). Animals (Basel) 2024; 14:1428. [PMID: 38791646 PMCID: PMC11117297 DOI: 10.3390/ani14101428] [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: 04/08/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Winter supplemental feeding (SF) is commonly used to improve the survival of captive wildlife. To investigate the impact of winter supplementation on the gut microbiota of wildlife, we assessed changes in the gut microbiota of red deer (Cervus elaphus) during the supplementary and non-supplementary feeding (NSF) groups using 16S rRNA sequencing technology. We found no significant differences in the diversity of the gut microbiota between SF and NSF except for the Simpson's index. However, the relative abundance of Bacteroidetes, Lentisphaerae, and Proteobacteria in the gut microbiota was significantly higher during SF. Further, genera such as Intestinimonas, Rikenella, Lawsonibacter, Muribaculum, and Papillibacter were more abundant during SF. Beta diversity analysis showed significant differences between SF and NSF. The microbes detected during SF were primarily associated with lipid metabolism, whereas those detected during NSF were linked to fiber catabolism. High-energy feed affects the gut microbial composition and function in red deer. During SF, the gut microbes in red deer were enriched in microorganisms associated with butyrate and lipid metabolism, such as R. microfusus, M. intestinale, and Papillibacter cinnamivorans. These gut microbes may be involved in ameliorating obesity associated with high-energy diets. In summary, SF is a reasonable and effective management strategy.
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Affiliation(s)
- Peng Zheng
- College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (P.Z.); (W.G.)
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Weizhen Gao
- College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (P.Z.); (W.G.)
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Shaobo Cong
- Xinjiang Tianshan Wildlife Park, Urumqi 830039, China;
| | - Lin Leng
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Tao Wang
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
| | - Lei Shi
- College of Animal Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (P.Z.); (W.G.)
- Key Laboratory of Ecological Adaptation and Evolution of Extreme Environment Biology in Xinjiang, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China; (L.L.); (T.W.)
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17
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Liang J, Zhang P, Chen L, Chang J, Zhang R, Zhang G, Tian Y. Effect of high corn straw loads on short-chain fatty acid production in semi-continuous rumen reactor. BIORESOURCE TECHNOLOGY 2024; 395:130396. [PMID: 38301941 DOI: 10.1016/j.biortech.2024.130396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Ruminal microorganisms can efficiently hydrolyze biomass waste for short-chain fatty acid (SCFA) production. However, the continuous SCFA production by ruminal microorganisms at high loads is unclear. In this study, the effectiveness of a rumen semi-continuous reactor at high load for SCFA production was explored. Results showed that SCFA concentration reached 13.3 g/L at 8 % (w/v) corn straw load. The higher the corn straw load, the lower the volatile solid removal. Rumen microbial community composition changed significantly with increasing corn straw load. A significant decrease in bacterial diversity and abundance was observed at 8 % corn straw load. Some core genera such as Prevotella, Saccharofermentans, and Ruminococcus significantly increased. As corn straw loads increased, the expression of functional genes related to hydrolysis and acidogenesis gradually increased. Thus, the 8.0 % load is suitable for SCFA production. These findings provide new insights into high load fermentation of ruminal microorganisms.
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Affiliation(s)
- Jinsong Liang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Panyue Zhang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Le Chen
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Jianning Chang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Ru Zhang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China.
| | - Yu Tian
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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18
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Tang W, Xiang X, Wang H, Zhou W, He L, Yin Y, Li T. Zinc lactate alleviates oxidative stress by modulating crosstalk between constitutive androstane receptor signaling pathway and gut microbiota profile in weaned piglets. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 16:23-33. [PMID: 38131030 PMCID: PMC10730354 DOI: 10.1016/j.aninu.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 12/23/2023]
Abstract
This study aimed to determine the regulatory mechanism of dietary zinc lactate (ZL) supplementation on intestinal oxidative stress damage in a paraquat (PQ)-induced piglet model. Twenty-eight piglets (mean body weight 9.51 ± 0.23 kg) weaned at 28 d of age were randomly divided into control, ZL, PQ, and ZL + PQ groups (n = 7 in each group). The ZL-supplemented diet had little effect on growth performance under normal physiological conditions. However, under PQ challenge, ZL supplementation significantly improved average daily gain (P < 0.05) and reduced the frequency of diarrhea. ZL improved intestinal morphology and ultrastructure by significantly increasing the expression level of the jejunal tight junction protein, zonula occludens-1 (ZO-1) (P < 0.05), and intestinal zinc transport and absorption in PQ-induced piglets, which reduced intestinal permeability. ZL supplementation also enhanced the expression of antioxidant and anti-inflammatory factor-related genes and decreased inflammatory cytokine expression and secretion in PQ-induced piglets. Furthermore, ZL treatment significantly inhibited the activation of constitutive androstane receptor (CAR) signaling (P < 0.01) in PQ-induced piglets and altered the structure of the gut microbiota, especially by significantly increasing the abundance of beneficial gut microbes, including UCG_002, Ruminococcus, Rikenellaceae_RC9_gut_group, Christensenellaceae_R_7_group, Treponema, unclassified_Christensenellaceae, and unclassified_Erysipelotrichaceae (P < 0.05). These data reveal that pre-administration of ZL to piglets can suppress intestinal oxidative stress by improving antioxidant and anti-inflammatory capacity and regulating the crosstalk between CAR signaling and gut microbiota.
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Affiliation(s)
- Wenjie Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Sichuan Academy of Animal Sciences, Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animtech Feed Co., Ltd, Chengdu 610000, China
| | - Xuan Xiang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Houfu Wang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wentao Zhou
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Liuqin He
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiejun Li
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
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Gao SM, Fei HL, Li Q, Lan LY, Huang LN, Fan PF. Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations. Nat Commun 2024; 15:1254. [PMID: 38341424 PMCID: PMC10858875 DOI: 10.1038/s41467-024-45663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Han-Lan Fei
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
- College of Life Science, China West Normal University, Nanchong, 637002, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
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20
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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21
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Härer A, Rennison DJ. Gut Microbiota Uniqueness Is Associated with Lake Size, a Proxy for Diet Diversity, in Stickleback Fish. Am Nat 2024; 203:284-291. [PMID: 38306277 DOI: 10.1086/727703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
AbstractOrganismal divergence can be driven by differential resource use and adaptation to different trophic niches. Variation in diet is a major factor shaping the gut microbiota, which is crucial for many aspects of their hosts' biology. However, it remains largely unknown how host diet diversity affects the gut microbiota, and it could be hypothesized that trophic niche width is positively associated with gut microbiota diversity. To test this idea, we sequenced the 16S ribosomal RNA gene from intestinal tissue of 14 threespine stickleback populations from lakes of varying size on Vancouver Island, Canada, that have been shown to differ in trophic niche width. Using lake size as a proxy for trophic ecology, we found evidence for higher gut microbiota uniqueness among individuals from populations with broader trophic niches. While these results suggest that diet diversity might promote gut microbiota diversity, additional work investigating diet and gut microbiota variation of the same host organisms will be necessary. Yet our results motivate the question of how host population diversity (e.g., ecological, morphological, genetic) might interact with the gut microbiota during the adaptation to ecological niches.
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22
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Bambi M, Galla G, Donati C, Rovero F, Hauffe HC, Barelli C. Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance. Sci Rep 2024; 14:869. [PMID: 38195759 PMCID: PMC10776872 DOI: 10.1038/s41598-023-50126-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Although male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi (gut microbiota) in relation to habitat type has not been fully examined. To understand whether the combination of sex and habitat affects gut microbiota variation, we analyzed 40 fecal samples of wild yellow baboons (Papio cynocephalus) living in contrasting habitat types (intact, well-protected vs. fragmented, less protected forests) in the Udzungwa Mountains of Tanzania. Sex determination was performed using the marker genes SRY (Sex-determining Region Y) and DDX3X-DDX3Y (DEAD-Box Helicase 3). Samples were attributed to 34 individuals (19 females and 15 males) belonging to five social groups. Combining the results of sex determination with two amplicon sequencing datasets on bacterial (V1-V3 region of the 16S rRNA gene) and fungal (ITS2) gut communities, we found that overall, baboon females had a significantly higher gut bacterial richness compared to males. Beta diversity estimates indicated that bacterial composition was significantly different between males and females, and this was true for individuals from both well- and less protected forests. Our results highlight the combined role of sex and habitat type in shaping variation in gut microbial communities in wild non-human primates.
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Affiliation(s)
- Marina Bambi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudia Barelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
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23
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Amato KR, Pradhan P, Mallott EK, Shirola W, Lu A. Host-gut microbiota interactions during pregnancy. Evol Med Public Health 2024; 12:7-23. [PMID: 38288320 PMCID: PMC10824165 DOI: 10.1093/emph/eoae001] [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: 07/13/2022] [Revised: 11/07/2023] [Indexed: 01/31/2024] Open
Abstract
Mammalian pregnancy is characterized by a well-known suite of physiological changes that support fetal growth and development, thereby positively affecting both maternal and offspring fitness. However, mothers also experience trade-offs between current and future maternal reproductive success, and maternal responses to these trade-offs can result in mother-offspring fitness conflicts. Knowledge of the mechanisms through which these trade-offs operate, as well as the contexts in which they operate, is critical for understanding the evolution of reproduction. Historically, hormonal changes during pregnancy have been thought to play a pivotal role in these conflicts since they directly and indirectly influence maternal metabolism, immunity, fetal growth and other aspects of offspring development. However, recent research suggests that gut microbiota may also play an important role. Here, we create a foundation for exploring this role by constructing a mechanistic model linking changes in maternal hormones, immunity and metabolism during pregnancy to changes in the gut microbiota. We posit that marked changes in hormones alter maternal gut microbiome composition and function both directly and indirectly via impacts on the immune system. The gut microbiota then feeds back to influence maternal immunity and metabolism. We posit that these dynamics are likely to be involved in mediating maternal and offspring fitness as well as trade-offs in different aspects of maternal and offspring health and fitness during pregnancy. We also predict that the interactions we describe are likely to vary across populations in response to maternal environments. Moving forward, empirical studies that combine microbial functional data and maternal physiological data with health and fitness outcomes for both mothers and infants will allow us to test the evolutionary and fitness implications of the gestational microbiota, enriching our understanding of the ecology and evolution of reproductive physiology.
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Affiliation(s)
- Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Priyanka Pradhan
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wesley Shirola
- Department of Psychology, Northwestern University, Evanston, IL 60208, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
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24
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Mahmoudi M, Almario J, Lutap K, Nieselt K, Kemen E. Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues. ISME COMMUNICATIONS 2024; 4:ycae103. [PMID: 39165396 PMCID: PMC11333920 DOI: 10.1093/ismeco/ycae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024]
Abstract
Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here, we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and nonfungal eukaryotic communities colonizing the surface and endosphere of six wild Arabidopsis thaliana populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Among environmental factors, radiation- and humidity-related factors are the most important drivers of diversity patterns in the leaf, with stronger effects on epiphytic communities. Using linear models, we identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that environmental factors could impact interactions within microbial communities, we analyzed the seasonal patterns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at both micro (leaf compartment) and macro (site) scales. These findings could have practical implications for predicting and developing field-adapted microbes in the face of global change.
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Affiliation(s)
- Maryam Mahmoudi
- Microbial Interactions in Plant Ecosystems, IMIT/ZMBP, Eberhard Karls University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Juliana Almario
- Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Katrina Lutap
- Microbial Interactions in Plant Ecosystems, IMIT/ZMBP, Eberhard Karls University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, Eberhard Karls University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, IMIT/ZMBP, Eberhard Karls University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
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25
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Sun Y, Hao Y, Zhang Q, Liu X, Wang L, Li J, Li M, Li D. Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167079. [PMID: 37714349 DOI: 10.1016/j.scitotenv.2023.167079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.
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Affiliation(s)
- Yanfeng Sun
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China; Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang 050024, China
| | - Yaotong Hao
- Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China
| | - Qian Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xu Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Limin Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Juyong Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mo Li
- College of Life Sciences, Cangzhou Normal University, Cangzhou 061001, China.
| | - Dongming Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang 050024, China.
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26
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Härer A, Rennison DJ. The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals. mSphere 2023; 8:e0044223. [PMID: 38038446 PMCID: PMC10732045 DOI: 10.1128/msphere.00442-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.
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Affiliation(s)
- Andreas Härer
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
| | - Diana J. Rennison
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
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27
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Tang X, Zhang L, Ren S, Zhao Y, Zhang Y. Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas. Microbiol Spectr 2023; 11:e0002023. [PMID: 37815332 PMCID: PMC10715161 DOI: 10.1128/spectrum.00020-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Shi'en Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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28
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
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Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
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29
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Lin D, Hong J, Sanogo B, Du S, Xiang S, Hui JHL, Ding T, Wu Z, Sun X. Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations. MICROBIOME 2023; 11:267. [PMID: 38017581 PMCID: PMC10685545 DOI: 10.1186/s40168-023-01700-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/17/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails. RESULTS We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments. CONCLUSIONS Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.
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Affiliation(s)
- Datao Lin
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Benjamin Sanogo
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Parasitology, Institut National de Recherche en Sante Publique, Bamako, Mali
| | - Shuling Du
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China
| | - Suoyu Xiang
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China
| | - Jerome Ho-Lam Hui
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Ding
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
| | - Zhongdao Wu
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
| | - Xi Sun
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
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Mejia ME, Mercado-Evans V, Zulk JJ, Ottinger S, Ruiz K, Ballard MB, Fowler SW, Britton RA, Patras KA. Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model. NPJ Biofilms Microbiomes 2023; 9:87. [PMID: 37985659 PMCID: PMC10661851 DOI: 10.1038/s41522-023-00454-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (HMbmice). Like the community structure in conventional mice, HMbmice vaginal microbiota clustered into community state types but, uniquely, HMbmice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, HMbmice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous HMbmouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, HMbmice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.
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Affiliation(s)
- Marlyd E Mejia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Vicki Mercado-Evans
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Ottinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Korinna Ruiz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mallory B Ballard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Stephanie W Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Kathryn A Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA.
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31
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Rankins DR, Herrera MJ, Christensen MP, Chen A, Hood NZ, Heras J, German DP. When digestive physiology doesn't match "diet": Lumpenus sagitta (Stichaeidae) is an "omnivore" with a carnivorous gut. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111508. [PMID: 37625480 DOI: 10.1016/j.cbpa.2023.111508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
What an animal ingests and what it digests can be different. Thus, we examined the nutritional physiology of Lumpenus sagitta, a member of the family Stichaeidae, to better understand whether it could digest algal components like its better studied algivorous relatives. Although L. sagitta ingests considerable algal content, we found little evidence of algal digestion. This fish species has a short gut that doesn't show positive allometry with body size, low amylolytic activity that actually decreases as the fish grow, no ontogenetic changes in digestive enzyme gene expression, elevated N-acetyl-glucosaminidase activity (indicative of chitin breakdown), and an enteric microbial community that is consistent with carnivory and differs from members of its family that consume and digest algae. Hence, we are left concluding that L. sagitta is not capable of digesting the algae it consumes, and instead, are likely targeting epibionts on the algae itself, and other invertebrates consumed with the algae. Our study expands the coverage of dietary and digestive information for the family Stichaeidae, which is becoming a model for fish digestive physiology and genomics, and shows the power of moving beyond gut content analyses to better understand what an animal can actually digest and use metabolically.
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Affiliation(s)
- Daniel R Rankins
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA.
| | - Michelle J Herrera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Michelle P Christensen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Alisa Chen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Newton Z Hood
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Joseph Heras
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
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32
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Li D, Yang H, Li Q, Ma K, Wang H, Wang C, Li T, Ma Y. Prickly Ash Seeds improve immunity of Hu sheep by changing the diversity and structure of gut microbiota. Front Microbiol 2023; 14:1273714. [PMID: 38029081 PMCID: PMC10644117 DOI: 10.3389/fmicb.2023.1273714] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Prickly Ash Seeds (PAS), as a traditional Chinese medicinal herb, have pharmacological effects such as anti-asthma, anti-thrombotic, and anti-bacterial, but their impact on gut microbiota is still unclear. This study used a full-length 16 s rRNA gene sequencing technique to determine the effect of adding PAS to the diet on the structure and distribution of gut microbiota in Hu sheep. All lambs were randomly divided into two groups, the CK group was fed with a basal ration, and the LZS group was given a basal diet with 3% of PAS added to the ration. The levels of inflammatory factors (IL-10, IL-1β, and TNF-α) in intestinal tissues were measured by enzyme-linked immunosorbent assay (ELISA) for Hu sheep in the CK and LZS group. The results indicate that PAS can increase the diversity and richness of gut microbiota, and can affect the community composition of gut microbiota. LEfSe analysis revealed that Verrucomicrobiota, Kiritimatiella, WCHB 41, and uncultured_rumen_bacterium were significantly enriched in the LZS group. KEGG pathway analysis found that LZS was significantly higher than the CK group in the Excretory system, Folding, sorting and degradation, and Immune system pathways (p < 0.05). The results of ELISA assay showed that the level of IL-10 was significantly higher in the LZS group than in the CK group (p < 0.05), and the levels of TNF-α and IL-1β were significantly higher in the CK group than in the LZS group (p < 0.05). LEfSe analysis revealed that the dominant flora in the large intestine segment changed from Bacteroidota and Gammaproteobacteria to Akkermansiaceae and Verrucomicrobiae after PAS addition to Hu sheep lambs; the dominant flora in the small intestine segment changed from Lactobacillales and Aeriscardovia to Kiritimatiellae and WCHB1 41. In conclusion, the addition of PAS to sheep diets can increase the number and types of beneficial bacteria in the intestinal tract, improve lamb immunity, and reduce intestinal inflammation. It provides new insights into healthy sheep production.
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Affiliation(s)
- Dengpan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Hai Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Keyan Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Chunhui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
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33
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Tang X, Zhang L, Ren S, Zhao Y, Liu K, Zhang Y. Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas ( Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons. J Fungi (Basel) 2023; 9:1032. [PMID: 37888290 PMCID: PMC10607853 DOI: 10.3390/jof9101032] [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: 09/03/2023] [Revised: 10/05/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Shien Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Liu
- Qinghai Provincial Grassland Station, Xining 810008, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
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Klure DM, Dearing MD. Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents. FEMS Microbiol Ecol 2023; 99:fiad127. [PMID: 37838471 PMCID: PMC10622585 DOI: 10.1093/femsec/fiad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/22/2023] [Accepted: 10/11/2023] [Indexed: 10/16/2023] Open
Abstract
Gut microbes provide essential services to their host and shifts in their composition can impact host fitness. However, despite advances in our understanding of how microbes are assembled in the gut, we understand little about the stability of these communities within individuals, nor what factors influence its composition over the life of an animal. For this reason, we conducted a longitudinal survey of the gut microbial communities of individual free-ranging woodrats (Neotoma spp.) across a hybrid zone in the Mojave Desert, USA, using amplicon sequencing approaches to characterize gut microbial profiles and diet. We found that gut microbial communities were individualized and experienced compositional restructuring as a result of seasonal transitions and changes in diet. Turnover of gut microbiota was highest amongst bacterial subspecies and was much lower at the rank of Family, suggesting there may be selection for conservation of core microbial functions in the woodrat gut. Lastly, we identified an abundant core gut bacterial community that may aid woodrats in metabolizing a diet of plants and their specialized metabolites. These results demonstrate that the gut microbial communities of woodrats are highly dynamic and experience seasonal restructuring which may facilitate adaptive plasticity in response to changes in diet.
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Affiliation(s)
- Dylan M Klure
- School of Biological Sciences, University of Utah, 257 S 1400 E rm 201, Salt Lake City, UT, 84112, United States
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 S 1400 E rm 201, Salt Lake City, UT, 84112, United States
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35
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy. Int J Mol Sci 2023; 24:15201. [PMID: 37894882 PMCID: PMC10607084 DOI: 10.3390/ijms242015201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010 Alicante, Spain;
| | - María-Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Francisco Marco-Jiménez
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
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Li D, Xia W, Cui X, Zhao M, Huang K, Wang X, Shen J, Chen H, Zhu L. The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome. Evol Appl 2023; 16:1708-1720. [PMID: 38020871 PMCID: PMC10660799 DOI: 10.1111/eva.13595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 12/01/2023] Open
Abstract
Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.
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Affiliation(s)
- Dayong Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Wancai Xia
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Xinyuan Cui
- College of Life ScienceNanjing Normal UniversityNanjingChina
| | - Mei Zhao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Kai Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | - Xueyu Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Key Laboratory of Conservation Biology of Rhinopithecus roxellana (Department of Education of Sichuan Province)China West Normal UniversityNanchongChina
| | | | - Hua Chen
- Mingke BiotechnologyHangzhouChina
| | - Lifeng Zhu
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
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Li P, Hong J, Wu M, Yuan Z, Li D, Wu Z, Sun X, Lin D. Metagenomic Analysis Reveals Variations in Gut Microbiomes of the Schistosoma mansoni-Transmitting Snails Biomphalaria straminea and Biomphalaria glabrata. Microorganisms 2023; 11:2419. [PMID: 37894077 PMCID: PMC10609589 DOI: 10.3390/microorganisms11102419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
Biomphalaria snails play a crucial role in the transmission of the human blood fluke Schistosoma mansoni. The gut microbiota of intermediate hosts is known to influence their physiological functions, but little is known about its composition and role in Biomphalaria snails. To gain insights into the biological characteristics of these freshwater intermediate hosts, we conducted metagenomic sequencing on Biomphalaria straminea and B. glabrata to investigate variations in their gut microbiota. This study revealed that the dominant members of the gut microbiota in B. glabrata belong to the phyla Bacteroidetes and Proteobacteria, which were also found to be the top two most abundant gut bacteria in B. straminea. We identified Firmicutes, Acidovorax and Bosea as distinctive gut microbes in B. straminea, while Aeromonas, Cloacibacterium and Chryseobacterium were found to be dependent features of the B. glabrata gut microbiota. We observed significant differences in the community structures and bacterial functions of the gut microbiota between the two host species. Notably, we found a distinctive richness of antibiotic resistance genes (ARGs) associated with various classes of antibiotics, including bacitracin, chloramphenicol, tetracycline, sulfonamide, penicillin, cephalosporin_ii and cephalosporin_i, fluoroquinolone, aminoglycoside, beta-lactam, multidrug and trimethoprim, in the digestive tracts of the snails. Furthermore, this study revealed the potential correlations between snail gut microbiota and the infection rate of S. mansoni using Spearman correlation analysis. Through metagenomic analysis, our study provided new insights into the gut microbiota of Biomphalaria snails and how it is influenced by host species, thereby enhancing our understanding of variant patterns of gut microbial communities in intermediate hosts. Our findings may contribute to future studies on gastropod-microbe interactions and may provide valuable knowledge for developing snail control strategies to combat schistosomiasis in the future.
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Affiliation(s)
- Peipei Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou 510180, China
| | - Mingrou Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhanhong Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Dinghao Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
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Härer A, Rennison DJ. Assessing the validity of fecal sampling for characterizing variation in threespine stickleback's gut microbiota. PLoS One 2023; 18:e0290875. [PMID: 37733779 PMCID: PMC10513271 DOI: 10.1371/journal.pone.0290875] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
The gut microbiota is crucial for many aspects of their hosts' biology, and it has been characterized for many species across the animal kingdom. Yet, we still don't have a good understanding of whether non-lethal sampling can accurately capture the diversity of gut-associated bacterial communities, as estimated from lethal sampling of intestinal tissue. We further lack knowledge on whether non-lethal sampling methods are suitable for detecting gut microbiota shifts associated with changes in environmental factors (e.g., diet). We addressed these questions in threespine stickleback fish, a model system for evolutionary ecology, by comparing bacterial communities from intestinal tissue and feces. Despite some differences in community composition between the two sample types and considerable temporal variation among fecal samples, bacterial communities appear to largely overlap. Further, we detected consistent and significant changes of fecal bacterial communities associated with an experimental diet manipulation. This suggests that fecal sampling can represent an adequate non-lethal method to characterize the gut microbiota of threespine stickleback, but additional studies will be necessary before drawing general conclusions regarding the validity of fecal sampling for gut microbiota studies. To this end, we give recommendations to improve the characterization of the gut microbiota via fecal sampling. Fecal sampling allows studying temporal gut microbiota shifts associated with environmental change at the individual level, which increases opportunities for future experimental gut microbiota research.
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Affiliation(s)
- Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, California, United States of America
| | - Diana J. Rennison
- School of Biological Sciences, Department of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, California, United States of America
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Xi L, Han J, Wen X, Zhao L, Qin X, Luo S, Lv D, Song S. Species variations in the gut microbiota of captive snub-nosed monkeys. Front Endocrinol (Lausanne) 2023; 14:1250865. [PMID: 37780618 PMCID: PMC10534982 DOI: 10.3389/fendo.2023.1250865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Snub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments. Methods This study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies. Results The results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function. Discussion In conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.
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Affiliation(s)
- Li Xi
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- Henan Engineering Research Center of Development and Application of Green Feed Additives, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Jincheng Han
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- Henan Engineering Research Center of Development and Application of Green Feed Additives, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Xiaohui Wen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Longfei Zhao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Xinxi Qin
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Shengjun Luo
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dianhong Lv
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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40
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Williams CE, Williams CL, Logan ML. Climate change is not just global warming: Multidimensional impacts on animal gut microbiota. Microb Biotechnol 2023; 16:1736-1744. [PMID: 37247194 PMCID: PMC10443335 DOI: 10.1111/1751-7915.14276] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023] Open
Abstract
Climate change has rapidly altered many ecosystems, with detrimental effects for biodiversity across the globe. In recent years, it has become increasingly apparent that the microorganisms that live in and on animals can substantially affect host health and physiology, and the structure and function of these microbial communities can be highly sensitive to environmental variables. To date, most studies have focused on the effects of increasing mean temperature on gut microbiota, yet other aspects of climate are also shifting, including temperature variation, seasonal dynamics, precipitation and the frequency of severe weather events. This array of environmental pressures might interact in complex and non-intuitive ways to impact gut microbiota and consequently alter animal fitness. Therefore, understanding the impacts of climate change on animals requires a consideration of multiple types of environmental stressors and their interactive effects on gut microbiota. Here, we present an overview of some of the major findings in research on climatic effects on microbial communities in the animal gut. Although ample evidence has now accumulated that shifts in mean temperature can have important effects on gut microbiota and their hosts, much less work has been conducted on the effects of other climatic variables and their interactions. We provide recommendations for additional research needed to mechanistically link climate change with shifts in animal gut microbiota and host fitness.
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41
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Zhai J, Sun X, Lu R, Hu X, Huang Z. Bibliometric Analysis of Global Trends in Research on Seasonal Variations in Gut Microbiota from 2012 to 2022. Microorganisms 2023; 11:2125. [PMID: 37630685 PMCID: PMC10458723 DOI: 10.3390/microorganisms11082125] [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: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Seasons are the important influencing factor for gut microbiota, which in turn affects the ecology and evolution of the host. The seasonal variation in gut microbiota has increasingly attracted the attention of researchers and professionals worldwide. However, studies of seasonal variations in gut microbiota have not been systematically analyzed by bibliometrics or visual analysis. This study is based on 271 publications from 2012 to 2022 in the Web of Science Core Collection database (WOSCC) to analyze hot spots and trends in this field. The collaborations between different countries, institutions, authors, journals, and keywords were bibliometrically analyzed using Excel, CiteSpace (Version 6.2. R4), and VOSviewer (version 1.6.19) software. The number of publications has been increasing rapidly and shows a general upward trend. China and the Chinese Academy of Sciences are the country and institution contributing the most, respectively. The research hotspots and trends mainly include the diversity of gut microbiota communities in different seasons, the relationship between diet and gut microbiota in seasonal changes, and the relationship between gut microbiota and evolutionary adaptation in seasonal changes. This is the first bibliometric and visualization analysis of seasonal variations in gut microbiota, which may advance this field and lay the foundation for future research.
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Affiliation(s)
- Jiancheng Zhai
- Natural Reserve Planning and Research Institute, East China University of Technology, Nanchang 330013, China
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Xiao Sun
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330029, China
| | - Rui Lu
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Xueqin Hu
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Zhiqiang Huang
- Natural Reserve Planning and Research Institute, East China University of Technology, Nanchang 330013, China
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
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42
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Liu H, Li Y, Liang J, Nong D, Li Y, Huang Z. Evaluation of Gut Microbiota Stability and Flexibility as a Response to Seasonal Variation in the Wild François' Langurs (Trachypithecus francoisi) in Limestone Forest. Microbiol Spectr 2023; 11:e0509122. [PMID: 37404157 PMCID: PMC10433995 DOI: 10.1128/spectrum.05091-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/10/2023] [Indexed: 07/06/2023] Open
Abstract
The coevolution between gut microbiota and the host markedly influences the digestive strategies of animals to cope with changes in food sources. We have explored the compositional structure and seasonal variation in the gut microbiota of François' langur in a limestone forest in Guangxi, southwest China, using 16S rRNA sequencing. Our results demonstrated that Firmicutes and Bacteroidetes were the dominant phyla in langurs, followed by Oscillospiraceae, Christensenellaceae, and Lachnospiraceae at the family level. The top five dominant phyla did not show significant seasonal variations, and only 21 bacterial taxa differed at the family level, indicating stability in gut the microbiota possibly with respect to foraging for several dominant plants and high-leaf feeding by the langurs. Moreover, rainfall and minimum humidity are important factors affecting the gut microbiota of the langurs, but they explain few changes in bacterial taxa. The activity budget and thyroid hormone levels of the langurs did not differ significantly between seasons, indicating that these langurs did not respond to seasonal changes in food by regulating behavior or reducing metabolism. The present study indicates that the gut microbiota's structure is related to digestion and energy absorption of these langurs, providing new perspectives on their adaptation to limestone forests. IMPORTANCE François' langur is a primate that particularly lives in karst regions. The adaptation of wild animals to karst habitats has been a hot topic in behavioral ecology and conservation biology. In this study, gut microbiota, behavior, and thyroid hormone data were integrated to understand the interaction of the langurs and limestone forests from the physiological response, providing basic data for assessing the adaptation of the langurs to the habitats. The responses of the langurs to environmental changes were explored from the seasonal variations in gut microbiota, which would help to further understand the adaptive strategies of species to environmental changes.
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Affiliation(s)
- Hongying Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Jipeng Liang
- Administration Center of Guangxi Chongzuo White-Headed Langur National Nature Reserve, Chongzuo, China
| | - Dengpan Nong
- Administration Center of Guangxi Chongzuo White-Headed Langur National Nature Reserve, Chongzuo, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
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Pacheco-Torres I, Hernández-Sánchez D, García-De la Peña C, Tarango-Arámbula LA, Crosby-Galván MM, Sánchez-Santillán P. Analysis of the Intestinal and Faecal Bacterial Microbiota of the Cervidae Family Using 16S Next-Generation Sequencing: A Review. Microorganisms 2023; 11:1860. [PMID: 37513032 PMCID: PMC10386072 DOI: 10.3390/microorganisms11071860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
The Cervidae family has a wide distribution due to its adaptation to numerous ecological environments, which allows it to develop a diverse microbial community in its digestive tract. Recently, research has focused on the taxonomic composition and functionality of the intestinal and faecal microbiota of different cervid species worldwide, as well as their microbial diversity and variation under different associated factors such as age, sex, diet, distribution, and seasonal variation. In addition, there is special interest in knowing how cervids act as reservoirs of zoonotic pathogenic microorganisms, which represent a threat to public health. This review provides a synthesis of the growing field of microbiota determination in cervids worldwide, focusing on intestinal and faecal samples using 16S next-generation sequencing. It also documents factors influencing microbial diversity and composition, the microorganisms reported as pathogenic/zoonotic, and the perspectives regarding the conservation of these species. Knowing the interactions between bacteria and cervid health can drive management and conservation strategies for these species and help develop an understanding of their evolutionary history and the interaction with emerging disease-causing microorganisms.
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Affiliation(s)
| | | | | | | | | | - Paulino Sánchez-Santillán
- Faculty of Veterinary Medicine and Zootechnics No. 2, Autonomous University of Guerrero, Cuajinicuilapa 41940, Mexico
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Yang S, Zheng J, He S, Yuan Z, Wang R, Wu D. Exploring the elevation dynamics of rumen bacterial communities in Barn feeding cattle from 900 to 3,600 meters by full-length 16S sequencing. Front Vet Sci 2023; 10:1169573. [PMID: 37533459 PMCID: PMC10390322 DOI: 10.3389/fvets.2023.1169573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
The diversity and abundance of rumen microorganisms serve as indicators not only of the host's digestive and metabolic capacity but also of its health status. The complex microbial communities in the rumen are influenced to varying degrees by environmental adaptability. In this study, we collected 24 rumen fluid samples from 24 healthy male cattle in three regions of Yunnan, China. Using 16S rRNA amplicon sequencing data analysis, we examined the variations in rumen microorganisms among cattle fed at altitudes of 900 m, 1800 m, and 3,600 m. Altitude-related environmental factors did not surpass phylogeny as the main driving force behind the convergent evolution of yellow cattle rumen microbiome composition. However, they did have an impact on the alpha diversity of the rumen microbiome and the coevolution of the core microbiome. The change in altitude noticeably influenced the diversity and richness of the rumen microbiota, highlighting the environmental effect of altitude. As altitude increased, there was an observed increase in the abundance of Firmicutes and Bacteroidetes, while the abundance of ruminal Proteobacteria and Kiritimatiellaeota decreased. Importantly, at the genus level, the core genus exhibited distinct dynamic changes as altitude increased. Ruminants exhibit the ability to adapt their gut type in accordance with altitude, thereby optimizing energy utilization, especially in high-altitude settings. These discoveries offer valuable insights into the coevolution of host-microbe interactions during ruminant adaptation to various altitudinal environments.
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Affiliation(s)
- Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Jieyi Zheng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Shichun He
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Zaimei Yuan
- Kunming Animal Disease Prevention and Control Center, Kunming, China
| | - Rongjiao Wang
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Dongwang Wu
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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Chen X, Chen Y, Lin H, Liu Z, Peng C, Xu X, Jia J, Zhang M, Liu C. In situ and self-adaptive BOD bioreaction sensing system based on environmentally domesticated microbial populations. Talanta 2023; 261:124671. [PMID: 37201342 DOI: 10.1016/j.talanta.2023.124671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/11/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023]
Abstract
Biochemical oxygen demand (BOD) is a water quality parameter of vital importance. Rapid BOD analysis methods have emerged to simplify the five-day BOD (BOD5) measurement protocol. However, their universal implementations are restricted by the tricky environmental matrix (including environmental microbes, contaminants, ionic compositions, etc.). Here, an in situ and self-adaptive BOD bioreaction sensing system consisting of a "gut-like" microfluidic coil bioreactor with self-renewed biofilm was proposed for the establishment of a rapid, resilient and reliable BOD determination method. With the spontaneous surface adhesion of environmental microbial populations, the biofilm was colonized in situ on the inner surface of the microfluidic coil bioreactor. Exploiting the environmental domestication during every real sample measurement, the biofilm was capable of self-renewal to adapt to the environmental changes and exhibited representative biodegradation behaviors. The aggregated abundant, adequate and adapted microbial populations in the BOD bioreactor rendered a total organic carbon (TOC) removal rate of 67.7% within a short hydraulic retention time of 99 s. As validated by an online BOD prototype, exceptional analytical performance was achieved in terms of reproducibility (relative standard deviation of 3.7%), survivability (inhibition by pH and metal ion interference of <20%) and accuracy (relative error of -5.9% to 9.7%). This work rediscovered the interactive effects of the environmental matrix on BOD assays and demonstrated an instructive attempt by making use of the environment to develop practical online BOD monitoring devices for water quality assessments.
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Affiliation(s)
- Xiaoting Chen
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Yiyuan Chen
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Huizhen Lin
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Ziye Liu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Ci'en Peng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Xiaolong Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Jianbo Jia
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Mengchen Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Changyu Liu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
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Mo F, Li Y, Liu Z, Zheng J, Huang Z. Captivity restructures the gut microbiota of François' langurs ( Trachypithecus francoisi). Front Microbiol 2023; 14:1166688. [PMID: 37250037 PMCID: PMC10218129 DOI: 10.3389/fmicb.2023.1166688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Gut microbiota is crucial to primate survival. Data on the gut microbiota of captive and wild animals can provide a physiological and ecological basis for the conservation of rare and endangered species. To study the effect of captivity on the gut microbiota, we examine the difference in the gut microbiota composition between captive and wild Francois' langurs (Trachypithecus francoisi), using 16S rRNA sequencing technology. The results showed that the composition of the gut microbiota of captive and wild langurs was characterized by Firmicutes (51.93 ± 10.07% vs. 76.15 ± 8.37%) and Bacteroidetes (32.43 ± 10.00% vs. 4.82 ± 1.41%) at the phylum level and was characterized by Oscillospiraceae (15.80 ± 5.19% vs. 30.21 ± 4.87%) at the family level. The alpha diversity of gut microbiota in captive langurs was higher than those in wild, such as the Shannon index (4.45 ± 0.33 vs. 3.98 ± 0.19, P < 0.001) and invSimpson index (35.11 ± 15.63 vs. 19.02 ± 4.87, P < 0.001). Principal coordinates analysis (PCoA) results showed significant differences in the composition of gut microbiota between captive and wild langurs at both the phylum and family levels (weight UniFrac algorithm, phylum level: R2 = 0.748, P = 0.001; family level: R2 = 0.685, P = 0.001). The relative abundance of Firmicutes (51.93 ± 10.07%) in captive langurs was lower than that of wild langurs (76.15 ± 8.37%), and the relative abundance of Bacteroidetes (32.43 ± 10.00%) in captive langurs was higher than that of wild (4.82 ± 1.41%). Our study concludes that dietary composition could be a crucial determinant in shaping the gut microbiota of langurs because more fiber-rich foods used by the wild langurs could increase the abundance of Firmicutes, and more simple carbohydrate-rich foods consumed by the captive langurs increase the abundance of Bacteroidetes. We highlight the importance of captivity on the gut microbiota and the need to consider the gut microbiota in animal provision.
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Affiliation(s)
- Fengxiang Mo
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zheng Liu
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Jingjin Zheng
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhonghao Huang
- Key Laboratory of Ecology and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
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48
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Tong Q, Dong WJ, Xu MD, Hu ZF, Guo P, Han XY, Cui LY. Characteristics and a comparison of the gut microbiota in two frog species at the beginning and end of hibernation. Front Microbiol 2023; 14:1057398. [PMID: 37206336 PMCID: PMC10191234 DOI: 10.3389/fmicb.2023.1057398] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/21/2023] [Indexed: 05/21/2023] Open
Abstract
Season has been suggested to contribute to variation in the gut microbiota of animals. The complicated relationships between amphibians and their gut microbiota and how they change throughout the year require more research. Short-term and long-term hypothermic fasting of amphibians may affect gut microbiota differently; however, these changes have not been explored. In this study, the composition and characteristics of the gut microbiota of Rana amurensis and Rana dybowskii during summer, autumn (short-term fasting) and winter (long-term fasting) were studied by high-throughput Illumina sequencing. Both frog species had higher gut microbiota alpha diversity in summer than autumn and winter, but no significant variations between autumn and spring. The summer, autumn, and spring gut microbiotas of both species differed, as did the autumn and winter microbiomes. In summer, autumn and winter, the dominant phyla in the gut microbiota of both species were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. All animals have 10 OTUs (>90% of all 52 frogs). Both species had 23 OTUs (>90% of all 28 frogs) in winter, accounting for 47.49 ± 3.84% and 63.17 ± 3.69% of their relative abundance, respectively. PICRUSt2 analysis showed that the predominant functions of the gut microbiota in these two Rana were focused on carbohydrate metabolism, Global and overview maps, Glycan biosynthesis metabolism, membrane transport, and replication and repair, translation. The BugBase analysis estimated that among the seasons in the R. amurensis group, Facultatively_Anaerobic, Forms_Biofilms, Gram_Negative, Gram_Positive, Potentially_Pathogenic were significantly different. However, there was no difference for R. dybowskii. The research will reveal how the gut microbiota of amphibians adapts to environmental changes during hibernation, aid in the conservation of endangered amphibians, particularly those that hibernate, and advance microbiota research by elucidating the role of microbiota under various physiological states and environmental conditions.
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Affiliation(s)
- Qing Tong
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Wen-jing Dong
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
| | - Ming-da Xu
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
| | - Zong-fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Peng Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-yun Han
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
| | - Li-yong Cui
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
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49
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Li Q, Fei HL, Luo ZH, Gao SM, Wang PD, Lan LY, Zhao XF, Huang LN, Fan PF. Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons. NPJ Biofilms Microbiomes 2023; 9:21. [PMID: 37085482 PMCID: PMC10121652 DOI: 10.1038/s41522-023-00388-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Wild animals may encounter multiple challenges especially food shortage and altered diet composition in their suboptimal ranges. Yet, how the gut microbiome responds to dietary changes remains poorly understood. Prior studies on wild animal microbiomes have typically leaned upon relatively coarse dietary records and individually unresolved fecal samples. Here, we conducted a longitudinal study integrating 514 time-series individually recognized fecal samples with parallel fine-grained dietary data from two Skywalker hoolock gibbon (Hoolock tianxing) groups populating high-altitude mountainous forests in western Yunnan Province, China. 16S rRNA gene amplicon sequencing showed a remarkable seasonal fluctuation in the gibbons' gut microbial community structure both across individuals and between the social groups, especially driven by the relative abundances of Lanchnospiraceae and Oscillospiraceae associated with fluctuating consumption of leaf. Metagenomic functional profiling revealed that diverse metabolisms associated with cellulose degradation and short-chain fatty acids (SCFAs) production were enriched in the high-leaf periods possibly to compensate for energy intake. Genome-resolved metagenomics further enabled the resolving metabolic capacities associated with carbohydrate breakdown among community members which exhibited a high degree of functional redundancy. Our results highlight a taxonomically and functionally sensitive gut microbiome actively responding to the seasonally shifting diet, facilitating the survival and reproduction of the endangered gibbon species in their suboptimal habitats.
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Affiliation(s)
- Qi Li
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Han-Lan Fei
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
- College of Life Science, China West Normal University, 637002, Nanchong, P.R. China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Pan-Deng Wang
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P.R. China
| | - Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Xin-Feng Zhao
- School of Life Sciences, South China Normal University, 510631, Guangzhou, P.R. China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China.
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China.
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50
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Zhao J, Yao Y, Li D, Zhu W, Xiao H, Xie M, Xiong Y, Wu J, Ni Q, Zhang M, Xu H. Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta). NPJ Biofilms Microbiomes 2023; 9:20. [PMID: 37081021 PMCID: PMC10119431 DOI: 10.1038/s41522-023-00387-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO2 and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.
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Affiliation(s)
- Junsong Zhao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Wei Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongtao Xiao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ying Xiong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Jiayun Wu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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