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Mazorra-Alonso M, Peralta-Sánchez JM, Martín-Vivaldi M, Martínez-Bueno M, Gómez RN, Soler JJ. Volatiles of symbiotic bacterial origin explain ectoparasitism and fledging success of hoopoes. Anim Microbiome 2024; 6:26. [PMID: 38725090 PMCID: PMC11084096 DOI: 10.1186/s42523-024-00312-9] [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: 02/26/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Some parasites use olfactory cues to detect their hosts and, since bacterial symbionts are partially responsible for animal odours, they could influence host parasitism. By autoclaving nest materials of hoopoe (Upupa epops) nests before reproduction started, we explored the hypothetical links between host-associated bacteria, volatiles and parasitism. During the nestling stage, we (i) estimated the level of ectoparasitism by chewing lice (Suborder Mallophaga) in adult hoopoe females and by Carnus haemapterus flies in nestlings, and (ii) characterized microbial communities and volatile profiles of nest environments (nest material and nest cavity, respectively) and uropygial secretions. RESULTS Experimental nests had less diverse bacterial communities and more diverse volatile profiles than control nests, while occupants experienced lower intensity of parasitism in experimental than in control nests. The experiment also affected beta diversity of the microbial communities of nest material and of the volatiles of the nestling uropygial secretions. Moreover, microbial communities of uropygial secretions and of nest materials covaried with their volatile profiles, while the volatile profile of the bird secretions explained nest volatile profile. Finally, a subset of the volatiles and bacteria detected in the nest material and uropygial secretions were associated with the ectoparasitism intensity of both adult females and nestlings, and with fledging success. CONCLUSIONS These results show that a component of animal odours is linked with the microbial communities of the host and its reproductive environment, and emphasize that the associations between bacteria, ectoparasitism and reproductive success are partially mediated by volatiles of bacterial origin. Future work should focus on mechanisms underlying the detected patterns.
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Affiliation(s)
- Mónica Mazorra-Alonso
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain
| | | | - Manuel Martín-Vivaldi
- Departamento de Zoología, Universidad de Granada, Granada, Spain
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes. Universidad de Granada, Granada, Spain
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, Granada, Spain
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes. Universidad de Granada, Granada, Spain
| | - Rafael Núñez Gómez
- Servicio de Instrumentación Científica, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Juan José Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain.
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes. Universidad de Granada, Granada, Spain.
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2
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Tang L, Yan L, Jia H, Xiong Y, Ma X, Chu H, Sun Z, Wang L, Shalitanati M, Li K, Hu D, Zhang D. Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China. Integr Zool 2023; 18:1027-1040. [PMID: 36606497 DOI: 10.1111/1749-4877.12699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.
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Affiliation(s)
- Liping Tang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Huiping Jia
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu Xiong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xinping Ma
- Xinjiang Mountain Ungulate Nature Reserve Management Center, Urumqi, China
| | - Hongjun Chu
- Institute of Forestry Ecology, Xinjiang Academy of Forestry Sciences, Urumqi, China
| | - Zhicheng Sun
- Administrative Bureau of Dunhuang Xihu National Nature Reserve, Dunhuang, China
| | - Liang Wang
- Administration of Gansu Anxi Extra-arid Desert National Nature Reserve, Guazhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mubalake Shalitanati
- Xinjiang Uygur Autonomous Region Wild Horse Breeding Research Center, Urumqi, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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3
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Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [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: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
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4
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Bi M, Liu C, Wang Y, Liu SJ. Therapeutic Prospect of New Probiotics in Neurodegenerative Diseases. Microorganisms 2023; 11:1527. [PMID: 37375029 DOI: 10.3390/microorganisms11061527] [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: 05/06/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Increasing clinical and preclinical evidence implicates gut microbiome (GM) dysbiosis as a key susceptibility factor for neurodegenerative disorders, including Alzheimer's disease (AD) and Parkinson's disease (PD). In recent years, neurodegenerative diseases have been viewed as being driven not solely by defects in the brain, and the role of GM in modulating central nervous system function via the gut-brain axis has attracted considerable interest. Encouraged by current GM research, the development of new probiotics may lead to tangible impacts on the treatment of neurodegenerative disorders. This review summarizes current understandings of GM composition and characteristics associated with neurodegenerative diseases and research demonstrations of key molecules from the GM that affect neurodegeneration. Furthermore, applications of new probiotics, such as Clostridium butyricum, Akkermansia muciniphila, Faecalibacterium prausnitzii, and Bacteroides fragilis, for the remediation of neurodegenerative diseases are discussed.
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Affiliation(s)
- Mingxia Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
| | - Chang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Calle-García J, Ramayo-Caldas Y, Zingaretti LM, Quintanilla R, Ballester M, Pérez-Enciso M. On the holobiont 'predictome' of immunocompetence in pigs. Genet Sel Evol 2023; 55:29. [PMID: 37127575 PMCID: PMC10150480 DOI: 10.1186/s12711-023-00803-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. METHODS We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. RESULTS Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. CONCLUSIONS Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.
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Affiliation(s)
- Joan Calle-García
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - María Ballester
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain.
- ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
- Corteva Agriscience, Virtual Location, Bergen op Zoom, Indianapolis, 4611 BB, Netherlands.
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6
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Pan B, Han X, Yu K, Sun H, Mu R, Lian CA. Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River. Mol Ecol 2023; 32:1183-1196. [PMID: 36478318 DOI: 10.1111/mec.16812] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Fish represent a large part of the taxonomic diversity of vertebrates and are of high commercial value. However, the factors influencing the gut microbiota composition of freshwater fish over large spatial scales remain unclear. Therefore, this study explored gut microbiome diversity in 24 fish species from the Yellow River, which spans over 1500 km across China. The results showed that geographical distance, host phylogeny and diet significantly influenced gut microbial community diversity, whereas sex, body length and body weight had minimal influence. Geographical distance was the primary factor shaping gut microbiota, and dissimilarity in microbial community structure increased with an increase in geographical distance, which was mainly driven by dispersal limitation. The microbial communities were more homogeneous at higher host taxonomic resolutions due to the dominant role of homogeneous selection in community convergence. Phylosymbiosis was observed across all host species, with a stronger pattern in Cypriniformes, which harbour host-specific microbial taxa. Host diet explained little variation in gut microbiome diversity, although it was significant for all diversity metrics tested. These findings collectively suggest that the geographical and host-based patterns of fish gut microbiota tend to be shaped by different ecological forces across the Yellow River. The present work provides a robust assessment of multiple factors driving fish gut microbial community assembly and offers insight into the mechanisms underlying shifts in fish gut microbiota in rivers across large spatial scales.
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Affiliation(s)
- Baozhu Pan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Xu Han
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - He Sun
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Rong Mu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Chun-Ang Lian
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
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7
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Xia C, Su J, Liu C, Mai Z, Yin S, Yang C, Fu L. Human microbiomes in cancer development and therapy. MedComm (Beijing) 2023; 4:e221. [PMID: 36860568 PMCID: PMC9969057 DOI: 10.1002/mco2.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
Colonies formed by bacteria, archaea, fungi, and viral groups and their genomes, metabolites, and expressed proteins constitute complex human microbiomes. An increasing evidences showed that carcinogenesis and disease progression were link to microbiomes. Different organ sources, their microbial species, and their metabolites are different; the mechanisms of carcinogenic or procancerous are also different. Here, we summarize how microbiomes contribute to carcinogenesis and disease progression in cancers of the skin, mouth, esophagus, lung, gastrointestinal, genital, blood, and lymph malignancy. We also insight into the molecular mechanisms of triggering, promoting, or inhibiting carcinogenesis and disease progress induced by microbiomes or/and their secretions of bioactive metabolites. And then, the strategies of application of microorganisms in cancer treatment were discussed in detail. However, the mechanisms by which human microbiomes function are still poorly understood. The bidirectional interactions between microbiotas and endocrine systems need to be clarified. Probiotics and prebiotics are believed to benefit human health via a variety of mechanisms, in particular, in tumor inhibition. It is largely unknown how microbial agents cause cancer or how cancer progresses. We expect this review may open new perspectives on possible therapeutic approaches of patients with cancer.
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Affiliation(s)
- Chenglai Xia
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Jiyan Su
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Can Liu
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Zhikai Mai
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Shuanghong Yin
- Affiliated Foshan Maternity and Chlid Healthcare HospitalSouthern Medical University, Foshan, China; School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhouChina
| | - Chuansheng Yang
- Department of Head‐Neck and Breast SurgeryYuebei People's Hospital of Shantou UniversityShaoguanChina
| | - Liwu Fu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine; Guangdong Esophageal Cancer Institute; Sun Yat‐sen University Cancer CenterGuangzhouPeople's Republic of China
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8
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Zheng Y, Chen J, Wang X, Han L, Yang Y, Wang Q, Yu Q. Metagenomic and Transcriptomic Analyses Reveal the Differences and Associations Between the Gut Microbiome and Muscular Genes in Angus and Chinese Simmental Cattle. Front Microbiol 2022; 13:815915. [PMID: 35495650 PMCID: PMC9048903 DOI: 10.3389/fmicb.2022.815915] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Gut microbiome and heredity are two important factors affecting the intramuscular fat (IMF) of cattle, excluding age, sex, and nutrition. This study aimed at deciphering these two differences by analyzing the gut microbiome and intramuscular differentially expressed genes (DEGs) in the Angus and Chinese Simmental cattle. Feces and longissimus dorsi were collected from the two groups of animals (n = 20/group) for multiomics analysis. Angus holds a significantly higher diversity than Chinese Simmental, and the relative abundance of Roseburia, Prevotella, Coprococcus, etc., was obviously higher in Angus. Chinese Simmental had higher levels of isobutyrate, isovalerate, and valerate, although similar levels of acetate, propionate, and butyrate were observed for the two groups. The DEGs upregulated in Chinese Simmental were mainly involved in immune and inflammatory responses, while those in Angus were associated with the regulation of muscle system and myofibril. We finally identified 17 species, including Eubacterium rectale, etc., which were positively correlated to muscle and fat metabolism genes (MSTN, MYLPF, TNNT3, and FABP3/4) and illustrate the associations between them. Our study unveils the gut microbial differences and significant DEGs as well as their associations between the two breeds, providing valuable guidance for future mechanism research and development of intervention strategies to improve meat quality.
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Affiliation(s)
- Ya Zheng
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Juanjuan Chen
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Xiaoxuan Wang
- Gansu YaSheng Hiosbon Food Group Co., Ltd., Lanzhou, China
| | - Ling Han
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Yayuan Yang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Qi Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Qunli Yu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
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Xu F, Yang C, Tang M, Wang M, Cheng Z, Chen D, Chen X, Liu K. The Role of Gut Microbiota and Genetic Susceptibility in the Pathogenesis of Pancreatitis. Gut Liver 2021; 16:686-696. [PMID: 34911043 PMCID: PMC9474482 DOI: 10.5009/gnl210362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022] Open
Abstract
Pancreatitis is one of the most common inflammatory diseases of the pancreas caused by autodigestion induced by excessive premature protease activation. However, recognition of novel pathophysiological mechanisms remains a still challenge. Both genetic and environmental factors contribute to the pathogenesis of pancreatitis, and the gut microbiota is a potential source of an environmental effect. In recent years, several new frontiers in gut microbiota and genetic risk assessment research have emerged and improved the understanding of the disease. These investigations showed that the disease progression of pancreatitis could be regulated by the gut microbiome, either through a translocation influence or in a host immune response manner. Meanwhile, the onset of the disease is also associated with the heritage of a pathogenic mutation, and the disease progression could be modified by genetic risk factors. In this review, we focused on the recent advances in the role of gut microbiota in the pathogenesis of pancreatitis, and the genetic susceptibility in pancreatitis.
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Affiliation(s)
- Fumin Xu
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Chunmei Yang
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Mingcheng Tang
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Ming Wang
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhenhao Cheng
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Dongfeng Chen
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao Chen
- Department of Nuclear Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Kaijun Liu
- Department of Gastroenterology, Daping Hospital, Army Medical University, Chongqing, China
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10
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Wu J, Lang H, Mu X, Zhang Z, Su Q, Hu X, Zheng H. Honey bee genetics shape the strain-level structure of gut microbiota in social transmission. MICROBIOME 2021; 9:225. [PMID: 34784973 PMCID: PMC8597283 DOI: 10.1186/s40168-021-01174-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/14/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Honey bee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honey bees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of the queen, we hypothesize that the microbiota structure can be shaped by host genetics. RESULTS We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of bees from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and "sequence-discrete population" levels. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. Genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the alternative splicing of the gluR-B gene, which is associated with an increased GABA level in the brain. CONCLUSIONS Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honey bees have been used extensively as a model organism for social behaviors, genetics, and the gut microbiome. Further identification of host genetic function as a shaping force of microbial structure will advance our understanding of the host-microbe interactions. Video abstract.
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Affiliation(s)
- Jiaqiang Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaohuan Mu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Zijing Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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11
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Ramayo-Caldas Y, Zingaretti LM, Pérez-Pascual D, Alexandre PA, Reverter A, Dalmau A, Quintanilla R, Ballester M. Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs. Anim Microbiome 2021; 3:74. [PMID: 34689834 PMCID: PMC8543910 DOI: 10.1186/s42523-021-00138-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/12/2021] [Indexed: 01/13/2023] Open
Abstract
Background The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. Results To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h2; proportion of phenotypic variance explained by the host genetics) and microbiability (m2; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that was dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m2 (0.275) compared to h2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r = 0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r = -0.34) and between Megasphaera and serum concentration of haptoglobin (r = 0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively. Conclusions Overall, our findings reveal an important connection between gut microbiota composition and immunity traits in pigs, and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00138-9.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140, Caldes de Montbui, Barcelona, Spain.
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - David Pérez-Pascual
- Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
| | | | - Antonio Reverter
- CSIRO Agriculture and Food, St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antoni Dalmau
- Animal Welfare Subprogram, IRTA, 17121, Monells, Girona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140, Caldes de Montbui, Barcelona, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140, Caldes de Montbui, Barcelona, Spain.
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12
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Pérez-Enciso M, Zingaretti LM, Ramayo-Caldas Y, de Los Campos G. Opportunities and limits of combining microbiome and genome data for complex trait prediction. Genet Sel Evol 2021; 53:65. [PMID: 34362312 PMCID: PMC8344190 DOI: 10.1186/s12711-021-00658-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how useful can the microbiome be for complex trait prediction? Are estimates of microbiability reliable? Can the underlying biological links between the host’s genome, microbiome, and phenome be recovered? Methods Here, we address these issues by (i) developing a novel simulation strategy that uses real microbiome and genotype data as inputs, and (ii) using variance-component approaches (Bayesian Reproducing Kernel Hilbert Space (RKHS) and Bayesian variable selection methods (Bayes C)) to quantify the proportion of phenotypic variance explained by the genome and the microbiome. The proposed simulation approach can mimic genetic links between the microbiome and genotype data by a permutation procedure that retains the distributional properties of the data. Results Using real genotype and rumen microbiota abundances from dairy cattle, simulation results suggest that microbiome data can significantly improve the accuracy of phenotype predictions, regardless of whether some microbiota abundances are under direct genetic control by the host or not. This improvement depends logically on the microbiome being stable over time. Overall, random-effects linear methods appear robust for variance components estimation, in spite of the typically highly leptokurtic distribution of microbiota abundances. The predictive performance of Bayes C was higher but more sensitive to the number of causative effects than RKHS. Accuracy with Bayes C depended, in part, on the number of microorganisms’ taxa that influence the phenotype. Conclusions While we conclude that, overall, genome-microbiome-links can be characterized using variance component estimates, we are less optimistic about the possibility of identifying the causative host genetic effects that affect microbiota abundances, which would require much larger sample sizes than are typically available for genome-microbiome-phenome studies. The R code to replicate the analyses is in https://github.com/miguelperezenciso/simubiome. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00658-7.
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Affiliation(s)
- Miguel Pérez-Enciso
- ICREA, Passeig de Lluís Companys 23, 08010, Barcelona, Spain. .,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain. .,Dept. of Epidemiology & Biostatistics, and Dept. of Statistics & Probability, Michigan State University, East Lansing, MI, 48824, USA.
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.,Dept. of Epidemiology & Biostatistics, and Dept. of Statistics & Probability, Michigan State University, East Lansing, MI, 48824, USA
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Barcelona, Spain
| | - Gustavo de Los Campos
- Dept. of Epidemiology & Biostatistics, and Dept. of Statistics & Probability, Michigan State University, East Lansing, MI, 48824, USA
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13
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Lei Y, Tang L, Liu S, Hu S, Wu L, Liu Y, Yang M, Huang S, Tang X, Tang T, Zhao X, Vlodavsky I, Zeng S, Tang B, Yang S. Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration. MICROBIOME 2021; 9:115. [PMID: 34016163 PMCID: PMC8138927 DOI: 10.1186/s40168-021-01065-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/31/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND The endoglycosidase heparanase which degrades heparan sulfate proteoglycans, exerts a pro-inflammatory mediator in various inflammatory disorders. However, the function and underlying mechanism of heparanase in acute pancreatitis remain poorly understood. Here, we investigated the interplay between heparanase and the gut microbiota in the development of acute pancreatitis. METHODS Acute pancreatitis was induced in wild-type and heparanase-transgenic mice by administration of caerulein. The differences in gut microbiota were analyzed by 16S ribosomal RNA sequencing. Antibiotic cocktail experiment, fecal microbiota transplantation, and cohousing experiments were used to assess the role of gut microbiota. RESULTS As compared with wild-type mice, acute pancreatitis was exacerbated in heparanase-transgenic mice. Moreover, the gut microbiota differed between heparanase-transgenic and wild-type mice. Heparanase exacerbated acute pancreatitis in a gut microbiota-dependent manner. Specially, the commensal Parabacteroides contributed most to distinguish the differences between wild-type and heparanase-transgenic mice. Administration of Parabacteroides alleviated acute pancreatitis in wild-type and heparanase-transgenic mice. In addition, Parabacteroides produced acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration. CONCLUSIONS The gut-pancreas axis played an important role in the development of acute pancreatitis and the acetate produced by Parabacteroides may be beneficial for acute pancreatitis treatment. Video abstract.
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Affiliation(s)
- Yuanyuan Lei
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Li Tang
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Shuang Liu
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Shiping Hu
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
- Department of Gastroenterology, The 983rd Hospital of Chinese PLA Joint Logistics Support Force, Tianjin, 300142, China
| | - Lingyi Wu
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Yaojiang Liu
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Min Yang
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Shengjie Huang
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
- Department of Gastroenterology, Chongqing Medical University Affiliated Second Hospital, Chongqing, 400010, China
| | - Xuefeng Tang
- Department of Pathology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Tao Tang
- Laboratory Department, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Xiaoyan Zhao
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel
| | - Shuo Zeng
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China
| | - Bo Tang
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China.
| | - Shiming Yang
- Department of Gastroenterology, Third Military Medical University Second Affiliated Hospital, Chongqing, 400037, China.
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14
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Liu YX, Qin Y, Chen T, Lu M, Qian X, Guo X, Bai Y. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell 2021; 12:315-330. [PMID: 32394199 PMCID: PMC8106563 DOI: 10.1007/s13238-020-00724-8] [Citation(s) in RCA: 316] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/10/2020] [Indexed: 12/22/2022] Open
Abstract
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.
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Affiliation(s)
- Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yuan Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Chen
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Meiping Lu
- Department of Rheumatology Immunology & Allergy, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310053, China
| | - Xubo Qian
- Department of Rheumatology Immunology & Allergy, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310053, China
| | - Xiaoxuan Guo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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15
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Liu X, Ma Y, Wang J. Genetic variation and function: revealing potential factors associated with microbial phenotypes. BIOPHYSICS REPORTS 2021; 7:111-126. [PMID: 37288143 PMCID: PMC10235906 DOI: 10.52601/bpr.2021.200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/09/2021] [Indexed: 06/09/2023] Open
Abstract
Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.
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Affiliation(s)
- Xiaolin Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Lv BM, Quan Y, Zhang HY. Causal Inference in Microbiome Medicine: Principles and Applications. Trends Microbiol 2021; 29:736-746. [PMID: 33895062 DOI: 10.1016/j.tim.2021.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022]
Abstract
Microorganisms that colonize the mammalian skin and cavity play critical roles in various physiological functions of the host. Numerous studies have revealed strong associations between the microbiota and multiple diseases. However, association does not mean causation. To clarify the mechanisms underlying microbiota-mediated diseases, research is moving from associative analyses to causation studies. In this article, we first introduce the principles of the computational methods for causal inference, and then discuss the applications of these methods in microbiome medicine. Furthermore, we examine the reliability of theoretically inferred causality by the interventionist framework. Finally, we show the potential of confirmed causality in microbiota-targeted therapy, especially in personalized dietary intervention. We conclude that a comprehensive understanding of the causal relationships between diets, microbiota, host targets, and diseases is critical to future microbiome medicine.
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Affiliation(s)
- Bo-Min Lv
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China.
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17
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Mazorra-Alonso M, Tomás G, Soler JJ. Microbially Mediated Chemical Ecology of Animals: A Review of Its Role in Conspecific Communication, Parasitism and Predation. BIOLOGY 2021; 10:274. [PMID: 33801728 PMCID: PMC8065758 DOI: 10.3390/biology10040274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023]
Abstract
Microbial symbionts are nowadays considered of pivotal importance for animal life. Among the many processes where microorganisms are involved, an emerging research avenue focuses on their major role in driving the evolution of chemical communication in their hosts. Volatiles of bacterial origin may underlie chemical communication and the transfer of social information through signals, as well as inadvertent social information. We reviewed the role of microorganisms in animal communication between conspecifics, and, because the microbiome may cause beneficial as well as deleterious effects on their animal hosts, we also reviewed its role in determining the outcome of the interactions with parasites and predators. Finally, we paid special attention to the hypothetical role of predation and parasitism in driving the evolution of the animal microbiome. We highlighted the novelty of the theoretical framework derived from considering the microbiota of animals in scenarios of communication, parasitism, and predation. We aimed to encourage research in these areas, suggesting key predictions that need to be tested to better understand what is one of the main roles of bacteria in animal biology.
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Affiliation(s)
- Mónica Mazorra-Alonso
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, 04120 Almería, Spain
| | - Gustavo Tomás
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, 04120 Almería, Spain
- Unidad Asociada (Consejo Superior de Investigaciones Científicas): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071 Granada, Spain
| | - Juan José Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, 04120 Almería, Spain
- Unidad Asociada (Consejo Superior de Investigaciones Científicas): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071 Granada, Spain
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18
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Reverter A, Ballester M, Alexandre PA, Mármol-Sánchez E, Dalmau A, Quintanilla R, Ramayo-Caldas Y. A gene co-association network regulating gut microbial communities in a Duroc pig population. MICROBIOME 2021; 9:52. [PMID: 33612109 PMCID: PMC7898758 DOI: 10.1186/s40168-020-00994-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/29/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. RESULTS In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. CONCLUSIONS Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits. Video Abstract.
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Affiliation(s)
- Antonio Reverter
- CSIRO Agriculture and Food, St. Lucia, Brisbane, Queensland 4067 Australia
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140 Caldes de Montbui, Barcelona, Spain
| | | | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Dalmau
- Animal Welfare Subprogram, IRTA, 17121 Monells, Girona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140 Caldes de Montbui, Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140 Caldes de Montbui, Barcelona, Spain
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19
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Abstract
As human populations spread across the world, they adapted genetically to local conditions. So too did the resident microorganism communities that everyone carries with them. However, the collective influence of the diverse and dynamic community of resident microbes on host evolution is poorly understood. The taxonomic composition of the microbiota varies among individuals and displays a range of sometimes redundant functions that modify the physicochemical environment of the host and may alter selection pressures. Here we review known human traits and genes for which the microbiota may have contributed or responded to changes in host diet, climate, or pathogen exposure. Integrating host–microbiota interactions in human adaptation could offer new approaches to improve our understanding of human health and evolution.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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20
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Lee CY, Peralta-Sánchez JM, Martínez-Bueno M, Møller AP, Rabelo-Ruiz M, Zamora-Muñoz C, Soler JJ. The gut microbiota of brood parasite and host nestlings reared within the same environment: disentangling genetic and environmental effects. ISME JOURNAL 2020; 14:2691-2702. [PMID: 32681160 DOI: 10.1038/s41396-020-0719-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Gut microbiota are essential for host health and survival, but we are still far from understanding the processes involved in shaping their composition and evolution. Controlled experimental work under lab conditions as well as human studies pointed at environmental factors (i.e., diet) as the main determinant of the microbiota with little evidence of genetic effects, while comparative interspecific studies detected significant phylogenetic effects. Different species, however, also differ in diet, feeding behavior, and environmental characteristics of habitats, all of which also vary interspecifically, and, therefore, can potentially explain most of the detected phylogenetic patterns. Here, we take advantage of the reproductive strategy of avian brood parasites and investigate gut microbiotas (esophageal (food and saliva) and intestinal) of great spotted cuckoo (Clamator glandarius) and magpie (Pica pica) nestlings that grow in the same nests. We also estimated diet received by each nestling and explored its association with gut microbiota characteristics. Although esophageal microbiota of magpies and great spotted cuckoos raised within the same environment (nest) did not vary, the microbiota of cloacal samples showed clear interspecific differences. Moreover, diet of great spotted cuckoo and magpie nestlings explained the microbiota composition of esophageal samples, but not of cloaca samples. These results strongly suggest a genetic component determining the intestinal microbiota of host and parasitic bird species, indicating that interspecific differences in gut morphology and physiology are responsible for such interspecific differences.
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Affiliation(s)
- Chop Yan Lee
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain
| | | | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain.,Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875, Beijing, China
| | - Miguel Rabelo-Ruiz
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain
| | - Carmen Zamora-Muñoz
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain.,Departamento de Zoología, Universidad de Granada, 18071, Granada, Spain
| | - Juan José Soler
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain. .,Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain.
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Cao J, Zhang Y, Dai M, Xu J, Chen L, Zhang F, Zhao N, Wang J. Profiling of Human Gut Virome with Oxford Nanopore Technology. MEDICINE IN MICROECOLOGY 2020. [DOI: 10.1016/j.medmic.2020.100012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Ramayo-Caldas Y, Prenafeta-Boldú F, Zingaretti LM, Gonzalez-Rodriguez O, Dalmau A, Quintanilla R, Ballester M. Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution. Anim Microbiome 2020; 2:18. [PMID: 33499953 PMCID: PMC7807704 DOI: 10.1186/s42523-020-00038-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. RESULTS Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. CONCLUSIONS Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | | | - Laura M. Zingaretti
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - Olga Gonzalez-Rodriguez
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Antoni Dalmau
- Animal Welfare Subprogram, IRTA, 17121 Monells, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
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Tang L, Li Y, Srivathsan A, Gao Y, Li K, Hu D, Zhang D. Gut Microbiomes of Endangered Przewalski's Horse Populations in Short- and Long-Term Captivity: Implication for Species Reintroduction Based on the Soft-Release Strategy. Front Microbiol 2020; 11:363. [PMID: 32226419 PMCID: PMC7081077 DOI: 10.3389/fmicb.2020.00363] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
Captivity maybe the only choice for survival of many endangered vertebrates, and understanding its broad effects is important for animal management and conservation, including breeding endangered species for subsequent release. Extreme environmental changes during captivity may influence survival ability in the wild. Captivity decreases gut bacterial diversity in a wide range of animals. However, most studies directly compare animals living in captivity with those in the wild, and there is a lack of understanding of effects of gradient shift in lifestyle during species reintroduction based on the soft-release strategy, which involves a confinement period in a field enclosure. Here, we used 16S rRNA amplicon sequencing to analyze gut microbiomes of 11 captive and 12 semi-wild Przewalski’s horses (PH; Equus ferus przewalskii) under the same captivity environment, using fecal samples. A subset of samples with abundant extracted DNA (including 3 captive and 3 semi-wild individuals) was selected for whole-genome shotgun sequencing. We found that community diversity did not differ between the semi-wild PH and captive PH, but the semi-wild PH had significantly higher bacterial richness than those in captivity. Relative abundances of all dominant phyla were similar across the semi-wild or captive horses, while those of the non-dominant phyla Tenericutes and Proteobacteria were significantly higher in semi-wild PH than in captive PH. Beta diversity results indicated that bacterial communities of captives and semi-wild horses were clearly separated distinct when considering only composition. Functional profiling of the microbiomes revealed that the semi-wild and captive gut microbiomes were largely similar. However, semi-wild horse microbiomes had higher abundance of bacterial genes related to core metabolic processes, such as carbohydrates, amino acids, and nucleic acid metabolism. The study revealed that semi-wild PH could retain specific non-dominant bacteria and harbor a more diverse microbiome than the captive counterpart, and thus have higher metabolic potential to utilize the complex plants efficiently. These results indicate that change in host lifestyle may play a role in microbiome differentiation in the process of reintroduction, suggesting that a short period of time in captivity is acceptable for PH from the perspective of maintaining the richness of intestinal bacterial flora to some extent.
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Affiliation(s)
- Liping Tang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yimeng Li
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yunyun Gao
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Li
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
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Strengthening the functional research on the interaction between host genes and microbiota. SCIENCE CHINA-LIFE SCIENCES 2020; 63:929-932. [DOI: 10.1007/s11427-020-1650-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/05/2020] [Indexed: 12/11/2022]
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25
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Pepoyan AZ, Tsaturyan VV, Badalyan M, Weeks R, Kamiya S, Chikindas ML. Blood protein polymorphisms and the gut bacteria: impact of probiotic Lactobacillus acidophilus Narine on Salmonella carriage in sheep. Benef Microbes 2020; 11:183-189. [PMID: 32028777 DOI: 10.3920/bm2019.0138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Related to previous reports on correlations between an animal's genotype, its commensal microbiota, and the ability to resist infections, the aim of the current study was to investigate the associations between sheep genotype and 5-methylcytosine (5-mC) DNA methylation patterns, sheep genotype and cell surface hydrophobicity of sheep gut commensal bacteria. In addition, the effect of the probiotic Lactobacillus acidophilus strain INMIA 9602 Er 317/402 (probiotic formulation Narine) on Salmonella carriage in sheep at Armenian farms was also investigated. Allelotypes and genotypes of different pathogen-sensitive sheep breeds from Armenian farms were studied based on genetic markers of blood transferrin, albumin, and ceruloplasmin. Additionally, the differences between the breeds of Mazekh, Balbas, and Mazekh/Balbas hybrids were reported. The relationship between host sheep blood transferrin and albumin polymorphisms and cell surface hydrophobicity/5-mC DNA methylation patterns from the predominant gut commensal bacteria was shown. The Narine probiotic eliminates Salmonella from the sheep gut microbiota. At the same time, no significant changes in the percentage of 5-mC DNA methylation of predominant gut bacteria after probiotic administration were observed. The evaluation of bacterial cell surface hydrophobicity, the most significant factor affecting bacterial adhesion, as well as 5-mC DNA methylation, might be used for specific sheep husbandry/breeding programs. This study suggests that the commercial probiotic Narine could potentially be used to reduce Salmonella carriage in sheep.
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Affiliation(s)
- A Z Pepoyan
- Department of Food Safety and Biotechnology, Armenian National Agrarian University, 74 Teryan, 0009 Yerevan, Armenia
| | | | - M Badalyan
- Department of Food Safety and Biotechnology, Armenian National Agrarian University, 74 Teryan, 0009 Yerevan, Armenia
| | - R Weeks
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ 08901-8520, USA
| | - Sh Kamiya
- Kyorin University School of Medicine, 6-20-2 Shinkawa, Tokyo, Japan
| | - M L Chikindas
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ 08901-8520, USA.,Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344006, Russia
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Zhang T, Li Q, Cheng L, Buch H, Zhang F. Akkermansia muciniphila is a promising probiotic. Microb Biotechnol 2019; 12:1109-1125. [PMID: 31006995 PMCID: PMC6801136 DOI: 10.1111/1751-7915.13410] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Akkermansia muciniphila (A. muciniphila), an intestinal symbiont colonizing in the mucosal layer, is considered to be a promising candidate as probiotics. A. muciniphila is known to have an important value in improving the host metabolic functions and immune responses. Moreover, A. muciniphila may have a value in modifying cancer treatment. However, most of the current researches focus on the correlation between A. muciniphila and diseases, and little is known about the causal relationship between them. Few intervention studies on A. muciniphila are limited to animal experiments, and limited studies have explored its safety and efficacy in humans. Therefore, a critical analysis of the current knowledge in A. muciniphila will play an important foundation for it to be defined as a new beneficial microbe. This article will review the bacteriological characteristics and safety of A. muciniphila, as well as its causal relationship with metabolic disorders, immune diseases and cancer therapy.
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Affiliation(s)
- Ting Zhang
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Qianqian Li
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Lei Cheng
- Biogas Institute of Ministry of Agriculture and Rural AffairsChengdu610041China
- Center for Anaerobic Microbial Resources of Sichuan ProvinceChengdu610041China
| | - Heena Buch
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Faming Zhang
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
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Knowles SCL, Eccles RM, Baltrūnaitė L. Species identity dominates over environment in shaping the microbiota of small mammals. Ecol Lett 2019; 22:826-837. [DOI: 10.1111/ele.13240] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/05/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022]
Affiliation(s)
- S. C. L. Knowles
- Department of Life Sciences Imperial College London Silwood Park Campus Buckhurst Road Ascot Berkshire UK
- Department of Pathobiology and Population Sciences The Royal Veterinary College Hawkshead Lane Hatfield HerfordshireAL9 7TA UK
| | - R. M. Eccles
- Centre for Genomic Research Biosciences Building Crown Street Liverpool L69 7ZB UK
| | - L. Baltrūnaitė
- Nature Research Centre Akademijos Str. 2 LT–08412 Vilnius Lithuania
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