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Liu Z, Wang P, Wei J, Li J, Luo X, Huang X, Zhang X, Li W, Qin Q. Effect of intestinal microbiota on adaptation to overcrowding stress in grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂). FISH & SHELLFISH IMMUNOLOGY 2025; 159:110165. [PMID: 39922247 DOI: 10.1016/j.fsi.2025.110165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/27/2025] [Accepted: 01/27/2025] [Indexed: 02/10/2025]
Abstract
Density is an important aquaculture parameter. When the pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) is farmed intensively, it could lead to a degradation in genetic resources and an increase in disease outbreaks. The composition of the intestinal microbiota plays a key role in creating a specific intestinal microecosystem, which is essential for the survival, growth, and immune response of the host under environmental stress like overcrowding. This study utilized 16S rRNA sequencing and metabolomics analysis techniques to investigate the differences in intestinal microbial community stability of grouper under different stocking time and density pressure conditions. The research results showed that compared to the low-density group, the high-density group of groupers experienced an increase in mortality rate and feed coefficient in the early stages of culture, while the weight gain rate decreased. Differential analysis of intestinal microbial communities revealed significant differences in the gut microbiota of grouper between different density groups after 10 days of culture, but no significant differences were observed after 20 days of culture. At the same time, intestinal histopathology showed that the high-density group of groupers exhibited a reduction in intestinal villi length and thickness of the intestinal wall after 10 days of culture. However, the intergroup differences had reduced after 20 days of culture. Furthermore, high density cultivation upregulated the expression of inflammatory factors like IL-1β, TNF-α, IL-8, and IL-6 in the intestinal tract of groupers after 10 days of culture. However, after 20 days of culture, the expression levels of intestinal inflammatory factors in both the high-density and low-density groups of groupers were significantly reduced, and the differences between the intergroup diminished. Through correlation analysis of differential metabolites and species in the intestine, multiple metabolites significantly upregulated and associated with the upregulation of the Staphylococcus genus were identified in the intestinal tract of groupers after 20 days of high-density cultivation. The selected four associated metabolites (including creatine, fosinopril, 4-aminobutyric acid, and guanidinopropanoic acid) were validated to significantly reduce the expression of cellular inflammatory factors using the self-established grouper head kidney (HK) cell line. In conclusion, density pressure in the early culture period could affect the stability of the intestinal microbial environment of grouper. As aquaculture time increases, the intestinal microbial community of grouper drives the body's anti-inflammatory response and enhanced its adaptation to density pressure by regulating own structure and secretion of metabolites.
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Affiliation(s)
- Zetian Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jingguang Wei
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jialing Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiaoqing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiaohong Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Zhang
- School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, Hainan Province, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 528478, China.
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Yang SY, Han SM, Lee JY, Kim KS, Lee JE, Lee DW. Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives. J Microbiol Biotechnol 2025; 35:e2412001. [PMID: 40223273 PMCID: PMC12010094 DOI: 10.4014/jmb.2412.12001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 02/14/2025] [Accepted: 02/24/2025] [Indexed: 04/15/2025]
Abstract
The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.
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Affiliation(s)
- So-Yeon Yang
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Seung Min Han
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji-Young Lee
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Kyoung Su Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Jae-Eun Lee
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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3
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Ma W, Han Z, Liu X, Cui W, Zhen D, Zhou X, Song Y, Jiang S. Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine. Microorganisms 2025; 13:731. [PMID: 40284568 PMCID: PMC12029867 DOI: 10.3390/microorganisms13040731] [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: 02/25/2025] [Accepted: 03/18/2025] [Indexed: 04/29/2025] Open
Abstract
The intestinal tract extends several times the length of bodies, with varying environmental conditions across different segments (small intestinal and large intestinal), thereby harboring distinct gut microbiota. Most studies focused on the quantitative responses of gut microbiota upon probiotics entering the gut, without an in-depth analysis of how the genetic change in local gut microbiota. Therefore, in this experiment, C57BL/6J male mice were once administered Lactiplantibacillus plantarum HNU082 (Lp082). Then, the mice were euthanized on the 1st, 3rd, and 7th days after gavage, and the contents of the small and large intestines of the mice were scraped for metagenomic analysis. Based on the characterization of large intestine and small intestine bacteria, changes in the diversity and abundance of single-nucleotide variants (SNVs) of microbiota were analyzed. There were observable distinct responses at the genetic level. A significant number of SNVs were identified in Ligilactobacillus murinus in the large intestine. These SNVs may impact the utilization of carbohydrates in L. murinus. Ingested probiotics traversed the entire gut and interacted with the indigenous microbiota, driving the evolution of the indigenous gut microbiota in the different intestinal segments, thereby influencing microbial growth and metabolism. This study investigates the role of probiotics in the evolution of gut microbiota. It offers new probiotic insights and a basis for targeted interventions.
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Affiliation(s)
| | | | | | | | | | | | | | - Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou 570228, China; (W.M.); (Z.H.); (X.L.); (W.C.); (D.Z.); (X.Z.); (Y.S.)
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4
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Guo Q, Wang G, Zheng L, Xue H, Wang R, Fang Y, Zhang J. A WYL domain transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP. Nat Commun 2025; 16:2193. [PMID: 40038299 PMCID: PMC11880434 DOI: 10.1038/s41467-025-57581-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 02/24/2025] [Indexed: 03/06/2025] Open
Abstract
Cyclic diguanosine monophosphate (c-di-GMP) functions as a crucial bacterial second messenger to control diverse biological functions. Although numerous studies have reported the health effects of Lactiplantibacillus plantarum, the regulatory role of c-di-GMP in L. plantarum remains elusive. Here we show that c-di-GMP functions as an important signal molecule for intestinal colonization of L. plantarum. The intracellular c-di-GMP pool in this probiotic is governed principally by the diguanylate cyclases DgcB, DgcC, and DgcD and the phosphodiesterases PdeA and PdeD. Moreover, we reveal that the WYL domain transcription factor MbpR is a c-di-GMP effector in L. plantarum WCFS1. MbpR reduces the transcription level of mucin-binding proteins (MucBPs) via binding to a special motif within the coding sequences. Perception of c-di-GMP by the WYL domain reversed the inhibitory effect of MbpR on the expression of MucBPs, resulting in increased adherence to intestinal epithelial cells by L. plantarum. Overall, our study provides evidence that a WYL domain transcription factor participates in probiotic colonization by sensing c-di-GMP.
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Affiliation(s)
- Quan Guo
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Hainan, China
| | - Guangqiang Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Leijie Zheng
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Hainan, China
| | - Hui Xue
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Hainan, China
| | - Ruimin Wang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Hainan, China
| | - Yajing Fang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Hainan, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China.
- Collaborative Innovation Center of One Health, Hainan University, Hainan, China.
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5
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Li Q, Li H, Tian L, Wang Y, Ouyang Z, Li L, Mao Y. Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene. ENVIRONMENT INTERNATIONAL 2025; 197:109334. [PMID: 39983413 DOI: 10.1016/j.envint.2025.109334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 02/05/2025] [Accepted: 02/14/2025] [Indexed: 02/23/2025]
Abstract
In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.
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Affiliation(s)
- Qihao Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, China
| | - Huixin Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, China
| | - Li Tian
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, China
| | - Yicheng Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, China
| | - Zeping Ouyang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, China
| | - Liguan Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong SAR, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, China.
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6
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Zhang Z, Guo Q, Yang Z, Sun Y, Jiang S, He Y, Li J, Zhang J. Bifidobacterium adolescentis-derived nicotinic acid improves host skeletal muscle mitochondrial function to ameliorate sarcopenia. Cell Rep 2025; 44:115265. [PMID: 39908139 DOI: 10.1016/j.celrep.2025.115265] [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: 08/16/2024] [Revised: 11/29/2024] [Accepted: 01/13/2025] [Indexed: 02/07/2025] Open
Abstract
Sarcopenia significantly diminishes quality of life and increases mortality risk in older adults. While the connection between the gut microbiome and muscle health is recognized, the underlying mechanisms are poorly understood. In this study, shotgun metagenomics revealed that Bifidobacterium adolescentis is notably depleted in individuals with sarcopenia, correlating with reduced muscle mass and function. This finding was validated in aged mice. Metabolomics analysis identified nicotinic acid as a key metabolite produced by B. adolescentis, linked to improvements in muscle mass and functionality in individuals with sarcopenia. Mechanistically, nicotinic acid restores nicotinamide adenine dinucleotide (NAD+) levels in muscle, inhibits the FoxO3/Atrogin-1/Murf-1 axis, and promotes satellite cell proliferation, reducing muscle atrophy. Additionally, NAD+ activation enhances the silent-information-regulator 1 (SIRT1)/peroxisome-proliferator-activated-receptor-γ-coactivator 1-alpha (PGC-1α) axis, stimulating mitochondrial biogenesis and promoting oxidative metabolism in slow-twitch fibers, ultimately improving muscle function. Our findings suggest that B. adolescentis-derived nicotinic acid could be a promising therapeutic strategy for individuals with sarcopenia.
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Affiliation(s)
- Zeng Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Quan Guo
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Zhihan Yang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Yukai Sun
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Shuaiming Jiang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Yangli He
- Department of Health Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, China
| | - Jiahe Li
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China; Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, Hainan, China.
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7
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Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O'Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RMT, Thinnes CC, Thiele I. A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. Cell Syst 2025; 16:101196. [PMID: 39947184 DOI: 10.1016/j.cels.2025.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 10/04/2024] [Accepted: 01/15/2025] [Indexed: 02/19/2025]
Abstract
Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland; Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Timothy Otto Hulshof
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Arianna Basile
- School of Medicine, University of Galway, Galway, Ireland; Department of Biology, University of Padova, Padova, Italy
| | | | | | | | | | | | - Ian Lalor
- University of Galway, Galway, Ireland
| | | | | | | | | | | | | | | | | | | | - Cyrille C Thinnes
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland; Ryan Institute, University of Galway, Galway, Ireland; Division of Microbiology, University of Galway, Galway, Ireland; APC Microbiome Ireland, Cork, Ireland.
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8
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Chen X, Yin X, Xu X, Zhang T. Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo. Nat Commun 2025; 16:1744. [PMID: 39966439 PMCID: PMC11836353 DOI: 10.1038/s41467-025-57088-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 02/11/2025] [Indexed: 02/20/2025] Open
Abstract
Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.
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Affiliation(s)
- Xi Chen
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.
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Liu X, Han Z, Ma W, Cui W, Zhen D, Jiang S, Zhang J. Effects of Lactiplantibacillus plantarum HNU082 intervention on fungi and bacteriophages in different intestinal segments of mice. BMC Microbiol 2025; 25:69. [PMID: 39922998 PMCID: PMC11806771 DOI: 10.1186/s12866-025-03784-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2024] [Accepted: 01/24/2025] [Indexed: 02/10/2025] Open
Abstract
BACKGROUND Gut fungi and bacteriophages, as members of the gut microbiota, can affect the interactions between gut bacteria and the host, participate in host metabolism, and are associated with various diseases. Probiotics substantially influence gut fungi and bacteriophages, modulating their composition through both direct and indirect mechanisms, thereby influencing host health. Current research primarily focuses on the effects of probiotics on the intestinal bacterial community. However, the alterations in the compositions of gut fungi and bacteriophages following probiotic intervention are not yet fully understood. Therefore, this study used Lactiplantibacillus plantarum HNU082 (Lp082) as the research subject and aimed to investigate the changes of the gut fungi and bacteriophages in the small intestine and the large intestine after the gavage of Lp082. RESULTS After probiotics entered the gut, the changes of the gut fungi and bacteriophages caused by the probiotics were more pronounced in the small intestine compared to the large intestine. The relative abundance of pathogenic fungi, such as Candida albicans, decreased in the small intestine. Furthermore, a strong positive correlation between the relative abundance of bacteriophages and their host bacteria in the gut was observed. The relative abundance of both Clostridia class bacteria and their bacteriophages increased. CONCLUSIONS In summary, the effects of probiotics on gut fungi and bacteriophages differed between the small intestine and the large intestine. This study contributed to a better understanding of the impact of probiotics on gut fungi and bacteriophages and provided data support for the association and dynamic changes between gut bacteria and their bacteriophages.
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Affiliation(s)
- Xinlei Liu
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China
| | - Zhe Han
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China
| | - Wenyao Ma
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China
| | - Weipeng Cui
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China
| | - Dongyu Zhen
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China
| | - Shuaiming Jiang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China.
| | - Jiachao Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, Hainan, China.
- Collaborative Innovation Center of One Health, Hainan University, Haikou, 570228, Hainan, China.
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10
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Bai D, Ma C, Xun J, Luo H, Yang H, Lyu H, Zhu Z, Gai A, Yousuf S, Peng K, Xu S, Gao Y, Wang Y, Liu Y. MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics. IMETA 2025; 4:e70002. [PMID: 40027478 PMCID: PMC11865346 DOI: 10.1002/imt2.70002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 01/21/2025] [Accepted: 01/23/2025] [Indexed: 03/05/2025]
Abstract
The rapid growth of microbiome research has generated an unprecedented amount of multi-omics data, presenting challenges in data analysis and visualization. To address these issues, we present MicrobiomeStatPlots, a comprehensive platform offering streamlined, reproducible tools for microbiome data analysis and visualization. This platform integrates essential bioinformatics workflows with multi-omics pipelines and provides 82 distinct visualization cases for interpreting microbiome datasets. By incorporating basic tutorials and advanced R-based visualization strategies, MicrobiomeStatPlots enhances accessibility and usability for researchers. Users can customize plots, contribute to the platform's expansion, and access a wealth of bioinformatics knowledge freely on GitHub (https://github.com/YongxinLiu/MicrobiomeStatPlot). Future plans include extending support for metabolomics, viromics, and metatranscriptomics, along with seamless integration of visualization tools into omics workflows. MicrobiomeStatPlots bridges gaps in microbiome data analysis and visualization, paving the way for more efficient, impactful microbiome research.
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Affiliation(s)
- Defeng Bai
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Chuang Ma
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- School of HorticultureAnhui Agricultural UniversityHefeiChina
| | - Jiani Xun
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Hao Luo
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Haifei Yang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- College of Life SciencesQingdao Agricultural UniversityQingdaoChina
| | - Hujie Lyu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Department of Food Science and NutritionThe Hong Kong Polytechnic UniversityHong KongSARChina
| | - Zhihao Zhu
- Zhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic MedicineGuangdong Medical UniversityZhanjiangChina
| | - Anran Gai
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- School of Agricultural SciencesZhengzhou UniversityZhengzhouChina
| | - Salsabeel Yousuf
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Kai Peng
- Jiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary MedicineYangzhou UniversityYangzhouChina
| | - Shanshan Xu
- School of Food and Biological EngineeringHefei University of TechnologyHefeiChina
| | - Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Yao Wang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yong‐Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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11
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Gao Y, Luo H, Lyu H, Yang H, Yousuf S, Huang S, Liu YX. Benchmarking short-read metagenomics tools for removing host contamination. Gigascience 2025; 14:giaf004. [PMID: 40036691 PMCID: PMC11878760 DOI: 10.1093/gigascience/giaf004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/31/2024] [Accepted: 01/09/2025] [Indexed: 03/06/2025] Open
Abstract
BACKGROUND The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences. RESULTS In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools. CONCLUSIONS Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.
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Affiliation(s)
- Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hao Luo
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hujie Lyu
- Department of Life Sciences, Imperial College of London, London SW7 2AZ, UK
| | - Haifei Yang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266000, China
| | - Salsabeel Yousuf
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yong-Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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12
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Wang H, Sun C, Li Y, Chen J, Zhao XM, Chen WH. Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners. MICROBIOME 2024; 12:260. [PMID: 39707560 DOI: 10.1186/s40168-024-01981-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 11/17/2024] [Indexed: 12/23/2024]
Abstract
BACKGROUND Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data. RESULTS We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins. CONCLUSIONS Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.
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Affiliation(s)
- Huarui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yun Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xing-Ming Zhao
- Department of Neurology, Institute of Science and Technology for Brain-Inspired Intelligence, Zhongshan Hospitaland, Fudan University , Shanghai, 200433, China.
- Lingang Laboratory, Shanghai, 200031, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang, 313000, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
- School of Biological Science, Jining Medical University, Rizhao, 276800, China.
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13
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Mi K, Xu R, Liu X. RFW captures species-level metagenomic functions by integrating genome annotation information. CELL REPORTS METHODS 2024; 4:100932. [PMID: 39662474 PMCID: PMC11704624 DOI: 10.1016/j.crmeth.2024.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 09/01/2024] [Accepted: 11/14/2024] [Indexed: 12/13/2024]
Abstract
Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.
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Affiliation(s)
- Kai Mi
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Rui Xu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China; The Second Affiliated Hospital of Nanjing Medical University, Nanjing 211166, China.
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14
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Peng Y, Zhu J, Wang S, Liu Y, Liu X, DeLeon O, Zhu W, Xu Z, Zhang X, Zhao S, Liang S, Li H, Ho B, Ching JYL, Cheung CP, Leung TF, Tam WH, Leung TY, Chang EB, Chan FKL, Zhang L, Ng SC, Tun HM. A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics. Cell Host Microbe 2024; 32:2212-2230.e8. [PMID: 39591974 DOI: 10.1016/j.chom.2024.10.017] [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: 07/16/2024] [Revised: 10/03/2024] [Accepted: 10/24/2024] [Indexed: 11/28/2024]
Abstract
Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.
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Affiliation(s)
- Ye Peng
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Jie Zhu
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Shilan Wang
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yingzhi Liu
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Xin Liu
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Orlando DeLeon
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, The University of Chicago, Chicago, IL 60637, USA
| | - Wenyi Zhu
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Xi Zhang
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Shilin Zhao
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Suisha Liang
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China
| | - Hang Li
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China
| | - Brian Ho
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China
| | - Jessica Yuet-Ling Ching
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ting Fan Leung
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Wing Hung Tam
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Eugene B Chang
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, The University of Chicago, Chicago, IL 60637, USA
| | - Francis Ka Leung Chan
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China.
| | - Siew Chien Ng
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR 999077, China.
| | - Hein Min Tun
- Microbiota I-Center (MagIC), Hong Kong SAR 999077, China; Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China.
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15
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Zhang Z, Fang Y, He Y, Farag MA, Zeng M, Sun Y, Peng S, Jiang S, Zhang X, Chen K, Xu M, Han Z, Zhang J. Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites. NPJ Biofilms Microbiomes 2024; 10:144. [PMID: 39632843 PMCID: PMC11618631 DOI: 10.1038/s41522-024-00618-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 11/20/2024] [Indexed: 12/07/2024] Open
Abstract
Sarcopenia is a major health challenge due to an aging population. Probiotics may improve muscle function through gut-muscle axis, but their efficacy and mechanisms in treating sarcopenia remain unclear. This study investigated the impact of Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) on old mice and sarcopenia patients. We analyzed 43 subjects, including gut microbiome, fecal metabolome, and serum metabolome, using a multi-omics approach to assess whether Probio-M8 can improve sarcopenia by modulating gut microbial metabolites. Probio-M8 significantly improved muscle function in aged mice and enhanced physical performance in sarcopenia patients. It reduced pathogenic gut species and increased beneficial metabolites such as indole-3-lactic acid, acetoacetic acid, and creatine. Mediating effect analyses revealed that Probio-M8 effectively reduced n-dodecanoyl-L-homoserine lactone level in gut concurrent with increased creatine circulation, to significantly enhance host physical properties. These findings provide new insights into probiotics as a potential treatment for sarcopenia by modulating gut microbiota metabolism.
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Affiliation(s)
- Zeng Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Yajing Fang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Yangli He
- Department of Health Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Egypt
| | - Min Zeng
- Department of Health Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Yukai Sun
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Siqi Peng
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Shuaiming Jiang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Xian Zhang
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Kaining Chen
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Meng Xu
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Zhe Han
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China.
- One Health Institute, Hainan University, Haikou, Hainan, China.
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16
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Zhang T, Li H, Jiang M, Hou H, Gao Y, Li Y, Wang F, Wang J, Peng K, Liu YX. Nanopore sequencing: flourishing in its teenage years. J Genet Genomics 2024; 51:1361-1374. [PMID: 39293510 DOI: 10.1016/j.jgg.2024.09.007] [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: 07/18/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024]
Abstract
Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As the nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.
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Affiliation(s)
- Tianyuan Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Hanzhou Li
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Mian Jiang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Huiyu Hou
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yali Li
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Fuhao Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Jun Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei 430000, China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225000, China
| | - Yong-Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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17
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Mi J, Jing X, Ma C, Shi F, Cao Z, Yang X, Yang Y, Kakade A, Wang W, Long R. A metagenomic catalogue of the ruminant gut archaeome. Nat Commun 2024; 15:9609. [PMID: 39505912 PMCID: PMC11542040 DOI: 10.1038/s41467-024-54025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 10/28/2024] [Indexed: 11/08/2024] Open
Abstract
While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.
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Affiliation(s)
- Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou, 730000, China.
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou, 730000, China.
| | - Xiaoping Jing
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Chouxian Ma
- Independent Researcher, Changsha, 410023, China
| | - Fuyu Shi
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ze Cao
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xin Yang
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yiwen Yang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Apurva Kakade
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Weiwei Wang
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Ruijun Long
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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18
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Chen T, Deng C, Li S, Li B, Liang Y, Zhang Y, Li J, Xu N, Yu K. Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135669. [PMID: 39208627 DOI: 10.1016/j.jhazmat.2024.135669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/30/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.
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Affiliation(s)
- Tianyi Chen
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, PR China
| | - Chunfang Deng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, PR China.
| | - Shaoyang Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Bing Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Yuanyan Zhang
- Jiangxi Academy of Eco-Environmental Sciences & Planning, Nanchang 330029, PR China
| | - Jiarui Li
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, PR China
| | - Nan Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
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19
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Kazantseva E, Donmez A, Frolova M, Pop M, Kolmogorov M. Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing. Nat Methods 2024; 21:2034-2043. [PMID: 39327484 DOI: 10.1038/s41592-024-02424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 08/22/2024] [Indexed: 09/28/2024]
Abstract
Bacterial species in microbial communities are often represented by mixtures of strains, distinguished by small variations in their genomes. Short-read approaches can be used to detect small-scale variation between strains but fail to phase these variants into contiguous haplotypes. Long-read metagenome assemblers can generate contiguous bacterial chromosomes but often suppress strain-level variation in favor of species-level consensus. Here we present Strainy, an algorithm for strain-level metagenome assembly and phasing from Nanopore and PacBio reads. Strainy takes a de novo metagenomic assembly as input and identifies strain variants, which are then phased and assembled into contiguous haplotypes. Using simulated and mock Nanopore and PacBio metagenome data, we show that Strainy assembles accurate and complete strain haplotypes, outperforming current Nanopore-based methods and comparable with PacBio-based algorithms in completeness and accuracy. We then use Strainy to assemble strain haplotypes of a complex environmental metagenome, revealing distinct strain distribution and mutational patterns in bacterial species.
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Affiliation(s)
- Ekaterina Kazantseva
- Bioinformatics and Systems Biology Program, ITMO University, St. Petersburg, Russia
| | - Ataberk Donmez
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Maria Frolova
- Functional Genomics of Prokaryotes Laboratory, Institute of Cell Biophysics, RAS, Pushchino, Russia
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, USA.
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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20
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Rajeev M, Jung I, Kang I, Cho JC. Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture. mSystems 2024; 9:e0078224. [PMID: 39315779 PMCID: PMC11494986 DOI: 10.1128/msystems.00782-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes. IMPORTANCE Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide.
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Affiliation(s)
- Meora Rajeev
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
- Institute for Specialized Teaching and Research, Inha University, Incheon, South Korea
| | - Ilsuk Jung
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Ilnam Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
- Center for Molecular and Cell Biology, Inha University, Incheon, South Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
- Center for Molecular and Cell Biology, Inha University, Incheon, South Korea
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21
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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024; 51:983-996. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [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: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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22
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Bai T, Shao H, Yang F, Zhang X, Tong P, Meng X, Wu Y, Chen H, Li X. Maternal High-Fat Diet Exacerbates Epicutaneous Sensitization and Oral Challenge-Induced Food Allergy to Ovalbumin in Offspring Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21240-21253. [PMID: 39261017 DOI: 10.1021/acs.jafc.4c05373] [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: 09/13/2024]
Abstract
Dietary factors have been associated with an increased prevalence of food allergy (FA). However, little is known about how an unhealthy diet in early life affects FA reactions in offspring. The objective of this study is to provide a scientific foundation for developing and promoting healthy dietary patterns in early life. In this study, we found that maternal high-fat diet (HFD) during pregnancy and lactation exacerbates FA (HFD-FA) in offspring mice, leading to increased serum levels of mast cell protease 1. First, we studied the systemic immunity of the HFD-FA mice and observed elevated levels of proinflammatory cytokines (IL-4, IL-6, and IL-1β) and a reduced frequency of Treg cells in splenocytes. Additionally, the HFD-FA mice showed increased gut permeability, accumulation of intestinal mast cells, and a decrease in the Treg cell frequency in the mesenteric lymph nodes. Furthermore, our findings also indicated a reduction in gut microbial diversity and abundance in HFD-FA mice. Importantly, lipid metabolism profiling revealed unique lipid profiles in the HFD-FA mice, with significant upregulation of triglycerides and downregulation of sphingolipids. Taken together, our results suggest that maternal HFD alters intestinal homeostasis and increases FA susceptibility in offspring mice.
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Affiliation(s)
- Tianliang Bai
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang 330031, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Huming Shao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang 330031, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Fan Yang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang 330031, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Xing Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang 330031, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Ping Tong
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang 330031, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Xuanyi Meng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330000, Jiangxi, China
| | - Yong Wu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330000, Jiangxi, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330000, Jiangxi, China
| | - Xin Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang 330031, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, Jiangxi, China
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23
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Kim N, Ma J, Kim W, Kim J, Belenky P, Lee I. Genome-resolved metagenomics: a game changer for microbiome medicine. Exp Mol Med 2024; 56:1501-1512. [PMID: 38945961 PMCID: PMC11297344 DOI: 10.1038/s12276-024-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 07/02/2024] Open
Abstract
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.
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Affiliation(s)
- Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Wonjong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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24
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Daisley B, Vancuren SJ, Brettingham DJL, Wilde J, Renwick S, Macpherson CV, Good DA, Botschner AJ, Yen S, Hill JE, Sorbara MT, Allen-Vercoe E. isolateR: an R package for generating microbial libraries from Sanger sequencing data. Bioinformatics 2024; 40:btae448. [PMID: 38991828 PMCID: PMC11254302 DOI: 10.1093/bioinformatics/btae448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/06/2024] [Accepted: 07/10/2024] [Indexed: 07/13/2024] Open
Abstract
MOTIVATION Sanger sequencing of taxonomic marker genes (e.g. 16S/18S/ITS/rpoB/cpn60) represents the leading method for identifying a wide range of microorganisms including bacteria, archaea, and fungi. However, the manual processing of sequence data and limitations associated with conventional BLAST searches impede the efficient generation of strain libraries essential for cataloging microbial diversity and discovering novel species. RESULTS isolateR addresses these challenges by implementing a standardized and scalable three-step pipeline that includes: (1) automated batch processing of Sanger sequence files, (2) taxonomic classification via global alignment to type strain databases in accordance with the latest international nomenclature standards, and (3) straightforward creation of strain libraries and handling of clonal isolates, with the ability to set customizable sequence dereplication thresholds and combine data from multiple sequencing runs into a single library. The tool's user-friendly design also features interactive HTML outputs that simplify data exploration and analysis. Additionally, in silico benchmarking done on two comprehensive human gut genome catalogues (IMGG and Hadza hunter-gather populations) showcase the proficiency of isolateR in uncovering and cataloging the nuanced spectrum of microbial diversity, advocating for a more targeted and granular exploration within individual hosts to achieve the highest strain-level resolution possible when generating culture collections. AVAILABILITY AND IMPLEMENTATION isolateR is available at: https://github.com/bdaisley/isolateR.
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Affiliation(s)
- Brendan Daisley
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dylan J L Brettingham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Simone Renwick
- Department of Pediatrics, School of Medicine, University of California, San Diego, United States
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), The Human Milk Institute (HMI), University of California, San Diego, CA 92093, United States
| | - Christine V Macpherson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - David A Good
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alexander J Botschner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sandi Yen
- Kennedy Institute of Rheumatology, Medical Sciences Division, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Matthew T Sorbara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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25
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Huang P, Dong Q, Wang Y, Tian Y, Wang S, Zhang C, Yu L, Tian F, Gao X, Guo H, Yi S, Li M, Liu Y, Zhang Q, Lu W, Wang G, Yang B, Cui S, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Ma B, Wu T, Zou H, Shi J, Zhang H, Fan D, Sheng Y, Zhao J, Tang L, Zhang H, Sun W, Chen W, Kong X, Chen L, Zhai Q. Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects. CELL GENOMICS 2024; 4:100559. [PMID: 38740021 PMCID: PMC11228888 DOI: 10.1016/j.xgen.2024.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/04/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.
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Affiliation(s)
- Pan Huang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yunfan Tian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoxiang Gao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hang Guo
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyang Li
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yang Liu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Gang Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Dongxu Hua
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Xiuchao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Yuwen Jiao
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Lu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Qiufeng Deng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Beining Ma
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Haifeng Zhang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yanhui Sheng
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liming Tang
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China.
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26
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [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: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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Goris T, Braune A. Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation. Microb Genom 2024; 10:001245. [PMID: 38785231 PMCID: PMC11170127 DOI: 10.1099/mgen.0.001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.
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Affiliation(s)
- Tobias Goris
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
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28
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Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen W, Zhao X. Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305818. [PMID: 38240578 PMCID: PMC10987132 DOI: 10.1002/advs.202305818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/01/2023] [Indexed: 04/04/2024]
Abstract
Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.
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Affiliation(s)
- Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Yanqi Dong
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Menglu Jin
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Senying Lai
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Longhao Jia
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Xueyang Zhao
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Huarui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Na L. Gao
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- Department of Laboratory MedicineZhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Peer Bork
- European Molecular Biology LaboratoryStructural and Computational Biology Unit69117HeidelbergGermany
- Max Delbrück Centre for Molecular Medicine13125BerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei University03722SeoulSouth Korea
- Department of BioinformaticsBiocenterUniversity of Würzburg97070WürzburgGermany
| | - Zhi Liu
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and Technology430074WuhanChina
| | - Wei‐Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
- Institution of Medical Artificial IntelligenceBinzhou Medical UniversityYantai264003China
| | - Xing‐Ming Zhao
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligenceand MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200433China
- State Key Laboratory of Medical NeurobiologyInstitute of Brain ScienceFudan UniversityShanghai200433China
- International Human Phenome Institutes (Shanghai)Shanghai200433China
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29
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Wang Y, Qu M, Bi Y, Liu WJ, Ma S, Wan B, Hu Y, Zhu B, Zhang G, Gao GF. The multi-kingdom microbiome catalog of the chicken gastrointestinal tract. BIOSAFETY AND HEALTH 2024; 6:101-115. [PMID: 40078943 PMCID: PMC11894977 DOI: 10.1016/j.bsheal.2024.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2025] Open
Abstract
Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries. We found that 812 and 240 MAGs in our dataset were putative novel species and genera, respectively, far beyond what was previously reported. The newly unclassified MAGs were predominant in Phyla Firmicutes_A (n = 263), followed by Firmicutes (n = 126), Bacteroidota (n = 121), and Proteobacteria (n = 87). Most of the classified species-level viral operational taxonomic units belong to Caudovirales. Approximately, 63.24 % of chicken gut viromes are predicted to infect two or more hosts, including complete circular viruses. Moreover, we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses. Together, our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date, functional insights into the chicken gastrointestinal tract microbiota, and paves the way for microbial interventions for better chicken health and productivity.
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Affiliation(s)
- Yanan Wang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Longhu Laboratory, Zhengzhou 450046, China
| | - Mengqi Qu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - William J. Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bo Wan
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- Longhu Laboratory, Zhengzhou 450046, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaiping Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- Longhu Laboratory, Zhengzhou 450046, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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30
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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31
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Wu S, Feng T, Tang W, Qi C, Gao J, He X, Wang J, Zhou H, Fang Z. metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model. Brief Bioinform 2024; 25:bbae085. [PMID: 38487846 PMCID: PMC10940841 DOI: 10.1093/bib/bbae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/26/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
Beneficial bacteria remain largely unexplored. Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model-based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains-derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae's potential marker. In different health-disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model-based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https://github.com/zhenchengfang/metaProbiotics.
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Affiliation(s)
- Shufang Wu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Feng
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Waijiao Tang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Cancan Qi
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Gao
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaolong He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaxuan Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhencheng Fang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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32
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Liu S, Zhang Z, Wang X, Ma Y, Ruan H, Wu X, Li B, Mou X, Chen T, Lu Z, Zhao W. Biosynthetic potential of the gut microbiome in longevous populations. Gut Microbes 2024; 16:2426623. [PMID: 39529240 PMCID: PMC11559365 DOI: 10.1080/19490976.2024.2426623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 09/26/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024] Open
Abstract
Gut microbiome plays a pivotal role in combating diseases and facilitating healthy aging, and natural products derived from biosynthetic gene clusters (BGCs) of the human microbiome exhibit significant biological activities. However, the natural products of the gut microbiome in long-lived populations remain poorly understood. Here, we integrated six cohorts of long-lived populations, encompassing a total of 1029 fecal metagenomic samples, and employed the metagenomic single sample assembled BGCs (MSSA-BGCs) analysis pipeline to investigate the natural products and their associated species. Our findings reveal that the BGC composition of the extremely long-lived group differed significantly from that of younger elderly and young individuals across five cohorts. Terpene and Type I PKS BGCs were enriched in the extremely long-lived, whereas cyclic-lactone-autoinducer BGCs were more prevalent in the young. Association analysis indicated that terpene BGCs were strongly associated with the abundance of Akkermansia muciniphila, which was also more abundant in the long-lived elderly across at least three cohorts. We assembled 18 A. muciniphila draft genomes using metagenomic data from the extremely long-lived group across six cohorts and discovered that they all harbor two classes of terpene BGCs, which aligns with the 97 complete genomes of A. muciniphila strains retrieved from the NCBI database. The core domains of these two BGC classes are squalene/phytoene synthases involved in the biosynthesis of tri- and tetraterpenes. Furthermore, the abundance of fecal A. muciniphila was significantly associated with eight types of triterpenoids. Targeted terpenoid metabolomic analysis revealed that two triterpenoids, Holstinone C and colubrinic acid, were enriched in the A. muciniphila culture solution compared to the medium, thereby confirming the production of triterpenoids by A. muciniphila. The natural products derived from the gut of long-lived populations provide intriguing indications of their potential beneficial roles in regulating health.
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Affiliation(s)
- Sheng Liu
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhao Zhang
- Research and Development Center, Center of Human Microecology Engineering and Technology of Guangdong Province, Guangzhou, Guangdong, China
| | - Xudong Wang
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yan Ma
- Research and Development Center, Center of Human Microecology Engineering and Technology of Guangdong Province, Guangzhou, Guangdong, China
| | - Hengfang Ruan
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xing Wu
- Research and Development Center, Center of Human Microecology Engineering and Technology of Guangdong Province, Guangzhou, Guangdong, China
| | - Baoxia Li
- Research and Development Center, Center of Human Microecology Engineering and Technology of Guangdong Province, Guangzhou, Guangdong, China
| | - Xiangyu Mou
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Tao Chen
- Research and Development Center, Center of Human Microecology Engineering and Technology of Guangdong Province, Guangzhou, Guangdong, China
| | - Zhengqi Lu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenjing Zhao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
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33
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Shen Z, Robert L, Stolpman M, Che Y, Allen KJ, Saffery R, Walsh A, Young A, Eckert J, Deming C, Chen Q, Conlan S, Laky K, Li JM, Chatman L, Kashaf SS, Kong HH, Frischmeyer-Guerrerio PA, Perrett KP, Segre JA. A genome catalog of the early-life human skin microbiome. Genome Biol 2023; 24:252. [PMID: 37946302 PMCID: PMC10636849 DOI: 10.1186/s13059-023-03090-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. RESULTS Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants. CONCLUSIONS Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.
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Affiliation(s)
- Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lukian Robert
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Milan Stolpman
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - You Che
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Katrina J Allen
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Richard Saffery
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Audrey Walsh
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Angela Young
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jana Eckert
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Qiong Chen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Karen Laky
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jenny Min Li
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Lindsay Chatman
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | | | - Kirsten P Perrett
- Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Allergy and Immunology, Royal Children's Hospital, Parkville, VIC, Australia
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
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Hai Q, Wang J, Kang W, Cheng S, Li J, Lyu N, Li Y, Luo Z, Liu Z. Metagenomic and metabolomic analysis of changes in intestinal contents of rainbow trout ( Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus at different culture water temperatures. Front Microbiol 2023; 14:1275649. [PMID: 37908544 PMCID: PMC10614001 DOI: 10.3389/fmicb.2023.1275649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Infectious hematopoietic necrosis (IHN) is a major disease that limits the culture of rainbow trout. In practical production, it has been found that the temperature of the culture water is a crucial factor affecting its mortality. Currently, little is known about how temperature affects the immune response of rainbow trout gut microbiota and metabolites to IHNV. In this study, our main objective is to analyze the changes in gut microorganisms of rainbow trout (juvenile fish with a consistent genetic background) after 14 days of infection with IHNV (5 × 105 pfu/fish) at 12-13°C (C: injected with saline, A: injected with IHNV) and 16-17°C (D: injected with saline, B: injected with IHNV) using metagenomic and metabolomic analyses, and to screen for probiotics that are effective against IHNV. The results showed that infection with IHNV at 12-13°C caused Eukaryote loss. Compared to Group C, Group A showed a significant increase in harmful pathogens, such as Yersiniaceae, and a significant alteration of 4,087 gut metabolites. Compared to group D, group B showed a significant increase in the abundance of Streptococcaceae and Lactococcus lactis, along with significant changes in 4,259 intestinal metabolites. Compared with their respective groups, the levels of two immune-related metabolites, 1-Octadecanoyl-glycero-3-phosphoethanolamine and L-Glutamate, were significantly upregulated in groups A and B. Compared to group B, Group A showed significantly higher pathogenic bacteria including Aeromonas, Pseudomonas, and Yersiniaceae, while group B showed a significant increase in Streptococcaceae and Lactococcus lactis. Additionally, there were 4,018 significantly different metabolites between the two groups. Interestingly, 1-Octadecanoyl-sn-glycero-3-phosphoethanolamine and L-Glutamate were significantly higher in group A than in group B. Some of the different metabolites in C vs. A are correlated with Fomitopsis pinicola, while in D vs. B they were correlated with Lactococcus raffinolactis, and in A vs. B they were correlated with Hypsizygus marmoreus. This study exposed how rainbow trout gut microbiota and metabolites respond to IHNV at different temperatures, and screens beneficial bacteria with potential resistance to IHN, providing new insights and scientific basis for the prevention and treatment of IHN.
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Affiliation(s)
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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35
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Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z, Chen S, Yao N, Gao NL, Xiao Q, Huang K, Wang X, Cui K, Rehman SU, Tang X, Liu D, Han H, Li Y, Chen WH, Liu Q. The multi-kingdom microbiome of the goat gastrointestinal tract. MICROBIOME 2023; 11:219. [PMID: 37779211 PMCID: PMC10544373 DOI: 10.1186/s40168-023-01651-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. RESULTS We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. CONCLUSIONS Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.
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Affiliation(s)
- Yanhong Cao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Guangxi Vocational University of Agriculture, Nanning, Guangxi, 530007, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Yingjian Wu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Teng Wang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zeyi Xuan
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Shaomei Chen
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na Yao
- Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, 530001, Guangxi, China
| | - Na L Gao
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Xiao
- Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, 570000, Hainan, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dewu Liu
- South China Agricultural University, Guangzhou, 510642, China
| | - Hongbing Han
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Wei-Hua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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Shen Z, Robert L, Stolpman M, Che Y, Walsh A, Saffery R, Allen KJ, Eckert J, Young A, Deming C, Chen Q, Conlan S, Laky K, Li JM, Chatman L, Saheb Kashaf S, NISC Comparative Sequencing Program, VITALITY team, Kong HH, Frischmeyer-Guerrerio PA, Perrett KP, Segre JA. A genome catalog of the early-life human skin microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541509. [PMID: 37398010 PMCID: PMC10312837 DOI: 10.1101/2023.05.22.541509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.
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Affiliation(s)
- Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Lukian Robert
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Milan Stolpman
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - You Che
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Audrey Walsh
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Richard Saffery
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Katrina J. Allen
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Jana Eckert
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Angela Young
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Qiong Chen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Karen Laky
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Jenny Min Li
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Lindsay Chatman
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | | | - VITALITY team
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | | | - Kirsten P. Perrett
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Allergy & Immunology, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
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Liu Y, Wang M, Li W, Gao Y, Li H, Cao N, Hao W, Zhao L. Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China. BMC Microbiol 2023; 23:102. [PMID: 37060052 PMCID: PMC10105465 DOI: 10.1186/s12866-023-02852-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 04/05/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Many studies reported the association between gut microbiota and type 2 diabetes mellitus (T2D), but it is still unclear which bacterial genus plays a key role and how the metabolic function of gut microbiota changes in the occurrence and development of T2D. Besides, there is a high diabetic prevalence in Mongolian population, which may be partly affected by their high calorie diet. This study identified the main bacterial genus influencing T2D in Mongolian population, and analyzed the changes of metabolic function of gut microbiome. The association between dietary factors and the relative abundance of main bacterial genus and its metabolic function was also studied. METHODS Dietary surveys and gut microbiota test were performed on 24 Mongolian volunteers that were divided into T2D (6 cases), PRET2D (6 cases) and Control group (12 cases) according to fasting plasma glucose (FPG) values. The relative abundance and metabolic function of gut microbiome from their fecal samples were measured by metagenomic analysis. Statistic method was used to evaluate the association between dietary factors and the relative abundance of the main bacterial genus or its metabolic function. RESULTS This study found that the Clostridium genus may be one of the key bacterial genera affecting the process of T2D. First, the relative abundance of Clostridium genus was significantly different among the three groups. Second, there was a higher relative abundance of metabolic enzymes of gut bacteria in PRET2D and T2D group than that in Control group. Third, a strong correlation between Clostridium genus and many metabolic enzymes was uncovered, many of which may be produced by the Clostridium. Last, carotene intake daily was negatively correlated with the Clostridium but positively correlated with tagaturonate reductase catalyzing interconversions of pentose and glucuronate. CONCLUSIONS The gut Clostridium genus may play an important role in the development of T2D and it could be a potential biomarker for T2D in Mongolian population. Meanwhile, the metabolic function of gut bacteria has changed during the early stage of T2D and the changes in carbohydrate, amino acid, lipid or energy metabolism of Clostridium genus may play a critical role. In addition, the carotene intake may affect reproduction and metabolic function of Clostridium genus.
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Affiliation(s)
- Yanchao Liu
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Mingxiao Wang
- Cspc Zhongqi Pharmaceutical Technology (Shijiazhuang) Co., Ltd, Shijiazhuang, Hebei Province, 050035, China
| | - Wuyuntana Li
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Yumin Gao
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Hailing Li
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Ning Cao
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Wenli Hao
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Lingyan Zhao
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China.
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China.
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