Microbiome最新文献

{"title":"Transgressive hybrids as hopeful holobionts.","authors":"Benjamin Thomas Camper, Andrew Stephen Kanes, Zachary Tyler Laughlin, Riley Tate Manuel, Sharon Anne Bewick","doi":"10.1186/s40168-024-01994-8","DOIUrl":"10.1186/s40168-024-01994-8","url":null,"abstract":"<p><strong>Background: </strong>Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying \"dead-end\" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful \"hopeful holobionts\" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses.</p><p><strong>Results: </strong>In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success.</p><p><strong>Conclusion: </strong>Transgressive segregation of HA microbiota traits is not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find b","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"19"},"PeriodicalIF":13.8,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11752726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143023683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.","authors":"Xiaozhen Liu, He Ding, Xiaoxue Zhang, Na Ta, Jinmei Zhao, Qian Zhang, Huiyun Liu, Mengjiao Sun, Xiaoqing Zhang","doi":"10.1186/s40168-024-02022-5","DOIUrl":"10.1186/s40168-024-02022-5","url":null,"abstract":"<p><strong>Background: </strong>While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.</p><p><strong>Results: </strong>A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness > 80% and contamination < 10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.</p><p><strong>Conclusions: </strong>These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"17"},"PeriodicalIF":13.8,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary diversification and succession of soil huge phages in glacier foreland.","authors":"Hu Liao, Jian Li, Yan-Zi Wang, Hu Li, Xin-Li An, Tao Wang, Rui-Ying Chang, Yong-Guan Zhu, Jian-Qiang Su","doi":"10.1186/s40168-024-02017-2","DOIUrl":"10.1186/s40168-024-02017-2","url":null,"abstract":"<p><strong>Background: </strong>Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.</p><p><strong>Results: </strong>Here, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.</p><p><strong>Conclusions: </strong>Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"18"},"PeriodicalIF":13.8,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.","authors":"Elena Rampanelli, Nadia Romp, Antonio Dario Troise, Jakshana Ananthasabesan, Hao Wu, Ismail Sahin Gül, Sabrina De Pascale, Andrea Scaloni, Fredrik Bäckhed, Vincenzo Fogliano, Max Nieuwdorp, Thi Phuong Nam Bui","doi":"10.1186/s40168-024-02002-9","DOIUrl":"10.1186/s40168-024-02002-9","url":null,"abstract":"<p><strong>Background: </strong>The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a prevalent commensal bacterium with the unique ability to convert dietary fructoselysine to butyrate, a well-known signaling molecule with proven health benefits. Dietary fructoselysine is an abundant Amadori product formed in foods during thermal treatment and is part of foods rich in dietary advanced glycation end products which have been associated with cardiometabolic disease. It is therefore of interest to investigate the causal role of this bacterium and fructoselysine metabolism in metabolic disorders.</p><p><strong>Results: </strong>We assessed associations of I. butyriciproducens with metabolic risk biomarkers at both strain and functional levels using a human cohort characterized by fecal metagenomic analysis. We observed that the level of the bacterial strain as well as fructoselysine fermentation genes were negatively associated with BMI, triglycerides, HbA1c, and fasting insulin levels. We also investigated the fructoselysine degradation capacity within the Intestinimonas genus using a culture-dependent approach and found that I. butyriciproducens is a key player in the butyrogenic fructoselysine metabolism in the gut. To investigate the function of I. butyriciproducens in host metabolism, we used the diet-induced obesity mouse model to mimic the human metabolic syndrome. Oral supplementation with I. butyriciproducens counteracted body weight gain, hyperglycemia, and adiposity. In addition, within the inguinal white adipose tissue, bacterial administration reduced inflammation and promoted pathways involved in browning and insulin signaling. The observed effects may be partly attributable to the formation of the short-chain fatty acids butyrate from dietary fructoselysine, as butyrate plasma and cecal levels were significantly increased by the bacterial strain, thereby contributing to the systemic effects of the bacterial treatment.</p><p><strong>Conclusions: </strong>I. butyriciproducens ameliorates host metabolism in the context of obesity and may therefore be a good candidate for new microbiota-therapeutic approaches to prevent or treat metabolic diseases. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"15"},"PeriodicalIF":13.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Akkermansia muciniphila and its metabolite propionic acid maintains neuronal mitochondrial division and autophagy homeostasis during Alzheimer's disease pathologic process via GPR41 and GPR43.","authors":"Zifan Wang, Cai Wang, Boyu Yuan, Li Liu, Haoming Zhang, Mingqiang Zhu, Hongxia Chai, Jie Peng, Yanhua Huang, Shuo Zhou, Juxiong Liu, Liyong Wu, Wei Wang","doi":"10.1186/s40168-024-02001-w","DOIUrl":"10.1186/s40168-024-02001-w","url":null,"abstract":"<p><strong>Background: </strong>Alzheimer's disease (AD) is a prevalent neurodegenerative disease (ND). In recent years, multiple clinical and animal studies have shown that mitochondrial dysfunction may be involved in the pathogenesis of AD. In addition, short-chain fatty acids (SCFA) produced by intestinal microbiota metabolism have been considered to be important factors affecting central nervous system (CNS) homeostasis. Among the main mediators of host-microbe interactions, volatile fatty acids play a crucial role. Nevertheless, the influence and pathways of microorganisms and their metabolites on Alzheimer's disease (AD) remain uncertain.</p><p><strong>Results: </strong>In this study, we present distinctions in blood and fecal SCFA levels and microbiota composition between healthy individuals and those diagnosed with AD. We found that AD patients showed a decrease in the abundance of Akkermansia muciniphila and a decrease in propionic acid both in fecal and in blood. In order to further reveal the effects and the mechanisms of propionic acid on AD prevention, we systematically explored the effects of propionic acid administration on AD model mice and cultured hippocampal neuronal cells. Results showed that oral propionate supplementation ameliorated cognitive impairment in AD mice. Propionate downregulated mitochondrial fission protein (DRP1) via G-protein coupled receptor 41 (GPR41) and enhanced PINK1/PARKIN-mediated mitophagy via G-protein coupled receptor 43 (GPR43) in AD pathophysiology which contribute to maintaining mitochondrial homeostasis both in vivo and in vitro. Administered A. muciniphila to AD mice before disease onset showed improved cognition, mitochondrial division and mitophagy in AD mice.</p><p><strong>Conclusions: </strong>Taken together, our results demonstrate that A. muciniphila and its metabolite propionate protect against AD-like pathological events in AD mouse models by targeting mitochondrial homeostasis, making them promising therapeutic candidates for the prevention and treatment of AD. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"16"},"PeriodicalIF":13.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation.","authors":"Roos-Marijn Berbers, Fernanda L Paganelli, Joris M van Montfrans, Pauline M Ellerbroek, Marco C Viveen, Malbert R C Rogers, Moniek Salomons, Jaap Schuurmans, Martine van Stigt Thans, Remi M M Vanmaris, Lodewijk A A Brosens, Maria Marlot van der Wal, Virgil A S H Dalm, P Martin van Hagen, Annick A J M van de Ven, Hae-Won Uh, Femke van Wijk, Rob J L Willems, Helen L Leavis","doi":"10.1186/s40168-024-01982-y","DOIUrl":"10.1186/s40168-024-01982-y","url":null,"abstract":"<p><strong>Background: </strong>Common variable immunodeficiency (CVID) is characterized by hypogammaglobulinemia and recurrent infections. Significant morbidity and mortality are caused by immune dysregulation complications (CVIDid), which affect around one-third of CVID patients and have a poorly understood etiology. Here, we investigate the hypothesis that gut microbial dysbiosis contributes to the inflammation underlying CVIDid.</p><p><strong>Results: </strong>Bacterial invasion of colonic crypts was observed in CVID (3/15) and X-linked agammaglobulinemia (XLA, 1/3), but not in healthy control (HC, 0/9) biopsies. Fecal gut microbiota was characterized using 16S rRNA-targeted amplicon sequencing. Increased bacterial load, decreased alpha diversity and distinct beta diversity were observed in CVIDid (n = 42) compared to HC (n = 48), and similar results were seen in CVID with IgA deficiency (n = 40) compared to HC. CVIDid and CVID-IgA showed enrichment of the genus Enterococcus, and in vitro studies confirmed the inflammatory potential of Enterococcus gallinarum and Enterococcus hirae in patient monocytes.</p><p><strong>Conclusions: </strong>This study further supports the hypothesis that a dysregulated gut microbiota, with IgA deficiency as an important driving factor, contributes to systemic inflammation in primary antibody deficiency, and introduces enterococci as potential pathobionts in CVIDid. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"12"},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rumen DNA virome and its relationship with feed efficiency in dairy cows.","authors":"Xiaohan Liu, Yifan Tang, Hongyi Chen, Jian-Xin Liu, Hui-Zeng Sun","doi":"10.1186/s40168-024-02019-0","DOIUrl":"10.1186/s40168-024-02019-0","url":null,"abstract":"<p><strong>Background: </strong>The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.</p><p><strong>Results: </strong>Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.</p><p><strong>Conclusions: </strong>This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"14"},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Core microbe Bifidobacterium in the hindgut of calves improves the growth phenotype of young hosts by regulating microbial functions and host metabolism.","authors":"Yimin Zhuang, Duo Gao, Wen Jiang, Yiming Xu, Guanglei Liu, Guobin Hou, Tianyu Chen, Shangru Li, Siyuan Zhang, Shuai Liu, Jingjun Wang, Jianxin Xiao, Mengmeng Li, Wei Wang, Shengli Li, Zhijun Cao","doi":"10.1186/s40168-024-02010-9","DOIUrl":"10.1186/s40168-024-02010-9","url":null,"abstract":"<p><strong>Background: </strong>The growth and health of young ruminants are regulated by their gut microbiome, which can have lifelong consequences. Compared with subjective grouping, phenotypic clustering might be a more comprehensive approach to revealing the relationship between calf growth state and core gut microbes. However, the identification of beneficial gut bacteria and its internal mechanisms of shaping host phenotype differentiation remains unclear.</p><p><strong>Results: </strong>In this study, calves were divided into two clusters, cluster1 and cluster2, based on 29 phenotypic indicators using cluster analysis. Calves in cluster2 showed better growth performance, including higher body weight (BW), average daily gain (ADG), and dry matter intake (DMI), as well as better serum indicators with a high level of total superoxide dismutase (T-SOD), interleukin-6 (IL-6), and insulin-like growth factor-1 (IGF-1) compared to those in cluster1. Multi-omics was used to detect microbial features among calves in different phenotypic clusters. Distinct differences were observed between the two clustered gut microbiomes, including microbial diversity and composition. The close relationships between growth performance, blood metabolites, and microbiome were also confirmed. In cluster2, Bifidobacterium members were the dominant contributors to microbial metabolic functions with a higher abundance. Furthermore, pathways involved in carbohydrate degradation, glycolysis, and biosynthesis of propionate and proteins were active, while methane production was inhibited. In addition, the diversity and richness of hindgut resistome in cluster2 were lower than those in cluster1. The isolation and culture of Bifidobacterium strain, as well as the mice experiment, indicated that B. longum 1109 from calf feces in cluster2 could promote the growth of young hosts, enhance their blood immunity and antioxidation, and improve the development of hindgut.</p><p><strong>Conclusions: </strong>In summary, cluster analysis has proved to be a feasible and reliable approach for identifying phenotypic subgroups of calves, prompting further exploration of host-microbiome interactions. Bifidobacterium as a core microbe in the hindgut of calves may play a crucial probiotic role in host phenotypic differentiation. This study enhances our comprehension of how gut core microbe shapes the host phenotype and provides new insights into the manipulation of beneficial gut colonizers to improve the growth performance and productivity of young ruminants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"13"},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef.","authors":"Marko Terzin, Steven J Robbins, Sara C Bell, Kim-Anh Lê Cao, Renee K Gruber, Pedro R Frade, Nicole S Webster, Yun Kit Yeoh, David G Bourne, Patrick W Laffy","doi":"10.1186/s40168-024-01972-0","DOIUrl":"10.1186/s40168-024-01972-0","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study reveals that functional information in reef-associated seawater microbes more robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"11"},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11737092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease.","authors":"Emmanouil Nychas, Andrea Marfil-Sánchez, Xiuqiang Chen, Mohammad Mirhakkak, Huating Li, Weiping Jia, Aimin Xu, Henrik Bjørn Nielsen, Max Nieuwdorp, Rohit Loomba, Yueqiong Ni, Gianni Panagiotou","doi":"10.1186/s40168-024-01990-y","DOIUrl":"10.1186/s40168-024-01990-y","url":null,"abstract":"<p><strong>Background: </strong>The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.</p><p><strong>Results: </strong>Here, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis. We identified highly specific microbiome signatures through building accurate machine learning models (accuracy = 0.845-0.917) for NAFLD with high portability (generalizable) and low prediction rate (specific) when applied to other metabolic diseases, as well as through a community approach involving differential co-abundance ecological networks. Moreover, using these signatures coupled with further mediation analysis and metabolic dependency modeling, we propose synergistic defined microbial consortia associated with NAFLD phenotype in overweight and lean individuals, respectively.</p><p><strong>Conclusion: </strong>Our study reveals robust and highly specific NAFLD signatures and offers a more realistic microbiome-therapeutics approach over individual species for this complex disease. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"10"},"PeriodicalIF":13.8,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}