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Wu Q, Li W, Kwok LY, Lv H, Sun J, Sun Z. Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut. Food Res Int 2024; 192:114840. [PMID: 39147525 DOI: 10.1016/j.foodres.2024.114840] [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: 03/19/2024] [Revised: 07/16/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Huimin Lv
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Jiaqi Sun
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China.
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Das A, Behera RN, Kapoor A, Ambatipudi K. The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17528-17542. [PMID: 37955263 DOI: 10.1021/acs.jafc.3c03834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The symbiosis of probiotic bacteria with humans has rendered various health benefits while providing nutrition and a suitable environment for their survival. However, the probiotics must survive unfavorable gut conditions to exert beneficial effects. The intrinsic resistance of probiotics to survive harsh conditions results from a myriad of proteins. Interaction of microbial proteins with the host is indispensable for modulating the gut microbiome, such as interaction with cell receptors and protective action against pathogens. The complex interplay of proteins should be unraveled by utilizing metaproteomic strategies. The contribution of probiotics to health is now widely accepted. However, due to the inconsistency of generalized probiotics, contemporary research toward precision probiotics has gained momentum for customized treatment. This review explores the application of metaproteomics and AI/ML algorithms in resolving multiomics data analysis and in silico prediction of microbial features for screening specific beneficial probiotic organisms. Implementing these integrative strategies could augment the potential of precision probiotics for personalized healthcare.
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Affiliation(s)
- Arpita Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ayushi Kapoor
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
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Wu D, Zhang C, Liu Y, Yao J, Yang X, Wu S, Du J, Yang X. Beyond faecal microbiota transplantation, the non-negligible role of faecal virome or bacteriophage transplantation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:893-908. [PMID: 36890066 DOI: 10.1016/j.jmii.2023.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/09/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
Intestinal microbiota, which contains bacteria, archaea, fungi, protists, and viruses including bacteriophages, is symbiotic and evolves together with humans. The balanced intestinal microbiota plays indispensable roles in maintaining and regulating host metabolism and health. Dysbiosis has been associated with not only intestinal diseases but other diseases such as neurology disorders and cancers. Faecal microbiota transplantation (FMT) or faecal virome or bacteriophage transplantation (FVT or FBT), transfers faecal bacteria or viruses, with a focus on bacteriophage, from one healthy individual to another individual (normally unhealthy condition), and aims to restore the balanced gut microbiota and assist in subduing diseases. In this review, we summarized the applications of FMT and FVT in clinical settings, discussed the advantages and challenges of FMT and FVT currently and proposed several considerations prospectively. We further provided our understanding of why FMT and FVT have their limitations and raised the possible future development strategy of FMT and FVT.
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Affiliation(s)
- Dengyu Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Juan Du
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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Abstract
A massive number of microorganisms, belonging to different species, continuously divide inside the guts of animals and humans. The large size of these communities and their rapid division times imply that we should be able to watch microbial evolution in the gut in real time, in a similar manner to what has been done in vitro. Here, we review recent findings on how natural selection shapes intrahost evolution (also known as within-host evolution), with a focus on the intestines of mice and humans. The microbiota of a healthy host is not as static as initially thought from the information measured at only one genomic marker. Rather, the genomes of each gut-colonizing species can be highly dynamic, and such dynamism seems to be related to the microbiota species diversity. Genetic and bioinformatic tools, and analysis of time series data, allow quantification of the selection strength on emerging mutations and horizontal transfer events in gut ecosystems. The drivers and functional consequences of gut evolution can now begin to be grasped. The rules of this intrahost microbiota evolution, and how they depend on the biology of each species, need to be understood for more effective development of microbiota therapies to help maintain or restore host health.
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Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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Abstract
Akkermansia muciniphila is a commensal bacterium using mucin as its sole carbon and nitrogen source. A. muciniphila is a promising candidate for next-generation probiotics to prevent inflammatory and metabolic disorders, including diabetes and obesity, and to increase the response to cancer immunotherapy. In this study, a comparative pan-genome analysis was conducted to investigate the genomic diversity and evolutionary relationships between complete genomes of 27 A. muciniphila strains, including KGMB strains isolated from healthy Koreans. The analysis showed that A. muciniphila strains formed two clades of group A and B in a phylogenetic tree constructed using 1,219 orthologous single-copy core genes. Interestingly, group A comprised of strains from human feces in Korea, whereas most of group B comprised strains from human feces in Europe and China, and from mouse feces. As group A and B branched, mucin hydrolysis played an important role in the stability of the core genome and drove evolution in the direction of defense against invading pathogens, survival in, and colonization in the mucus layer. In addition, WapA and anSME, which function in competition and post-translational modification of sulfatase, respectively, have been a particularly important selective pressure in the evolution of group A. KGMB strains in group A with anSME gene showed sulfatase activity, but KCTC 15667T in group B without anSME did not. Our findings revealed that KGMB strains evolved to gain an edge in the competition with other gut bacteria by increasing the utilization of sulfated mucin, which will allow it to become highly colonized in the gut environment.
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Affiliation(s)
- Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea,Department of Environmental Biotechnology, University of Science and Technology, Yuseong-gu, Republic of Korea,CONTACT Jung-Sook Lee Korean Collection for Type Cultures,Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si56212Republic of Korea
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