Microbiome最新文献

{"title":"F. prausnitzii potentially modulates the association between citrus intake and depression.","authors":"Chatpol Samuthpongtorn, Allison A Chan, Wenjie Ma, Fenglei Wang, Long H Nguyen, Dong D Wang, Olivia I Okereke, Curtis Huttenhower, Andrew T Chan, Raaj S Mehta","doi":"10.1186/s40168-024-01961-3","DOIUrl":"10.1186/s40168-024-01961-3","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome modulates the effects of diet on host health, but it remains unclear which specific foods and microbial features interact to influence risk of depression. To understand this interplay, we leveraged decades of dietary and depression data from a longitudinal cohort of women (n = 32,427), along with fecal metagenomics and plasma metabolomics from a substudy (n = 207) nested in this cohort, as well as an independent validation cohort of men (n = 307).</p><p><strong>Results: </strong>We report that citrus intake and its components are prospectively associated with a lower risk of depression and altered abundance of 15 gut microbial species, including enriched Faecalibacterium prausnitzii. In turn, we found a lower abundance of F. prausnitzii and its metabolic pathway, S-adenosyl-L-methionine (SAM) cycle I in participants with depression. To explore causality, we found that lower SAM production by F. prausnitzii may decrease intestinal monoamine oxidase A gene expression implicated in serotonin and dopamine synthesis.</p><p><strong>Conclusions: </strong>These data underscore the role of diet in the prevention of depression and offer a plausible explanation for how the intestinal microbiome modulates the influence of citrus on mental health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"237"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623783","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":"Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation.","authors":"Lukuan Huang, Ziyan Fan, Zhipeng Hu, Zhesi Li, Yingyi Fu, Qiong Wang, Xianyong Lin, Ying Feng","doi":"10.1186/s40168-024-01959-x","DOIUrl":"10.1186/s40168-024-01959-x","url":null,"abstract":"<p><strong>Background: </strong>Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome.</p><p><strong>Results: </strong>Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation.</p><p><strong>Conclusion: </strong>In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"236"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623791","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":"Unveiling bat-borne viruses: a comprehensive classification and analysis of virome evolution.","authors":"Yuyang Wang, Panpan Xu, Yelin Han, Wenliang Zhao, Lamei Zhao, Rui Li, Junpeng Zhang, Shuyi Zhang, Jian Lu, Peter Daszak, Qi Jin, Zhiqiang Wu","doi":"10.1186/s40168-024-01955-1","DOIUrl":"10.1186/s40168-024-01955-1","url":null,"abstract":"<p><strong>Background: </strong>Bats (Order Chiroptera) are an important reservoir of emerging zoonotic microbes, including viruses of public health concern such as henipaviruses, lyssaviruses, and SARS-related coronaviruses. Despite the continued discovery of new viruses in bat populations, a significant proportion of these viral agents remain uncharacterized, highlighting the imperative for additional research aimed at elucidating their evolutionary relationship and taxonomic classification.</p><p><strong>Results: </strong>In order to delve deeper into the viral reservoir hosted by bats, the present study employed Next Generation Sequencing (NGS) technology to analyze 13,105 swab samples obtained from various locations in China. Analysis of 378 sample pools revealed the presence of 846 vertebrate-associated viruses. Subsequent thorough examination, adhering to the International Committee on Taxonomy of Viruses (ICTV) criteria for virus classification, identified a total of 120 putative viral species with the potential to emerge as novel viruses, comprising a total of 294 viral strains. Phylogenetic analysis of conserved genomic regions indicated the novel virus exhibited a diverse array of viral lineages and branches, some of which displayed close genetic relationships to known human and livestock pathogens, such as poxviruses and pestiviruses.</p><p><strong>Conclusions: </strong>This study investigates the breadth of DNA and RNA viruses harbored by bats, delineating several novel evolutionary lineages and offering significant contributions to virus taxonomy. Furthermore, the identification of hitherto unknown viruses with relevance to human and livestock health underscores the importance of this study in encouraging infectious disease monitoring and management efforts in both public health and veterinary contexts. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"235"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623795","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":"Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils.","authors":"Xin-Di Zhao, Zi-Yu Gao, Jingjing Peng, Konstantinos T Konstantinidis, Si-Yu Zhang","doi":"10.1186/s40168-024-01952-4","DOIUrl":"10.1186/s40168-024-01952-4","url":null,"abstract":"<p><strong>Background: </strong>Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.</p><p><strong>Results: </strong>Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.</p><p><strong>Conclusions: </strong>Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"238"},"PeriodicalIF":13.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623797","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":"An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows.","authors":"Chenguang Zhang, Huifeng Liu, Xingwei Jiang, Zhihong Zhang, Xinfeng Hou, Yue Wang, Dangdang Wang, Zongjun Li, Yangchun Cao, Shengru Wu, Sharon A Huws, Junhu Yao","doi":"10.1186/s40168-024-01937-3","DOIUrl":"10.1186/s40168-024-01937-3","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The results indicated that the proportions of highly heritable subsets (h&lt;sup&gt;2&lt;/sup&gt; ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn&lt;sup&gt;2+&lt;/sup&gt; transport) (P &lt; 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp., Prevotella_sp._E15-22, Prevotella_sp._E13-27, which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) (P &lt; 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 (P &lt; 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp., which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;Our comprehensive study revealed the distinct heritability patterns of rumen microbial composition, function, and metabolism. Additionally, we shed light on the influence of host SNP variants on the rumen microbes with carbohydrate metabolism and their subsequent effects on lactation performance. Collectively, these findings offer compelling evidence for the host-microbe interactions, wherein cows active","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"232"},"PeriodicalIF":13.8,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623776","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":"Melatonin alleviates heat stress-induced spermatogenesis dysfunction in male dairy goats by regulating arachidonic acid metabolism mediated by remodeling the gut microbiota.","authors":"Xinrui Guo, Jing Xu, Yongkang Zhao, Jie Wang, Tingshu Fu, Mathias L Richard, Harry Sokol, Miao Wang, Yu Li, Yang Liu, Hui Wang, Chenlei Wang, Xueqin Wang, Haiyang He, Yazhou Wang, Baohua Ma, Sha Peng","doi":"10.1186/s40168-024-01942-6","DOIUrl":"10.1186/s40168-024-01942-6","url":null,"abstract":"<p><strong>Background: </strong>Heat stress (HS) commonly occurring in summer has gradually become a factor threatening the reproductive performance of male dairy goats by reducing their fecundity. Despite the melatonin is applied to relieve HS, it is still unclear whether melatonin protects against reproductive damage induced by HS in dairy goats and how it works. The purpose of the present study is to evaluate the role of melatonin in alleviating HS-induced spermatogenesis dysfunction in male dairy goats and further explore its mechanism.</p><p><strong>Results: </strong>HS impaired spermatogenesis, sperm formation in the testes, and sperm maturation in the epididymis of dairy goats, resulting in decreased sperm quality. Melatonin rescued the decrease of sperm quality induced by HS via decreasing inflammatory and oxidative stress levels in testicular tissue and enhancing intercellular barrier function within the testes. Amplicon-based microbiota analysis revealed that despite gut microbiota differences between melatonin-treated dairy goats and NC dairy goats to some extent, melatonin administration tends to return the gut microbiota of male dairy goats under HS to the levels of natural control dairy goats. To explore whether the protective role of melatonin in sperm quality is mediated by regulating gut microbiota, fecal microbiota of HS dairy goats with or without melatonin treatment were transferred to HS mice, respectively. We found HS mice that had received fecal bacteria of HS dairy goats experienced serious testicular injury and dyszoospermia, while this phenomenon was ameliorated in HS mice that had received fecal bacteria of dairy goats treated with melatonin, indicating melatonin alleviates HS-induced spermatogenic damage in a microbiota dependent manner. We further found that the testicular tissue of both HS dairy goats and mice transplanted with HS dairy goat feces produced large amounts of arachidonic acid (AA)-related metabolites, which were closely associated with semen quality. Consistently, supplementation with AA has been shown to elevate the levels of inflammation and oxidative stress in the testicular tissue of mice, disrupting intercellular connections and ultimately leading to spermatogenic disorders.</p><p><strong>Conclusion: </strong>This study has revealed that melatonin can effectively alleviate spermatogenic disorders in dairy goats caused by HS. This beneficial effect was primarily achieved through the modulation of gut microbiota, which subsequently inhibited the excessive synthesis of AA in testicular tissue. These discoveries are of great significance for preventing or improving the decline in male livestock reproductive performance caused by HS, enhancing the reproductive efficiency of elite male breeds, and ultimately improving the production efficiency of animal husbandry. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"233"},"PeriodicalIF":13.8,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623785","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":"Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes.","authors":"Neeraja Balasubrahmaniam, Jon C King, Bridget Hegarty, Karen C Dannemiller","doi":"10.1186/s40168-024-01915-9","DOIUrl":"10.1186/s40168-024-01915-9","url":null,"abstract":"<p><strong>Background: </strong>Increased risk of asthma and other respiratory diseases is associated with exposures to microbial communities growing in damp and moldy indoor environments. The exact causal mechanisms remain unknown, and occupant health effects have not been consistently associated with any species-based mold measurement methods. We need new quantitative methods to identify homes with potentially harmful fungal growth that are not dependent upon species. The goal of this study was to identify genes consistently associated with fungal growth and associated function under damp conditions for use as potential indicators of mold in homes regardless of fungal species present. A de novo metatranscriptomic analysis was performed using house dust from across the US, incubated at 50%, 85%, or 100% equilibrium relative humidity (ERH) for 1 week.</p><p><strong>Results: </strong>Gene expression was a function of moisture (adonis2 p < 0.001), with fungal metabolic activity increasing with an increase in moisture condition (Kruskal-Wallis p = 0.003). Genes associated with fungal growth such as sporulation (n = 264), hyphal growth (n = 62), and secondary metabolism (n = 124) were significantly upregulated at elevated ERH conditions when compared to the low 50% ERH (FDR-adjusted p ≤ 0.001, log2FC ≥ 2), indicating that fungal function is influenced by damp conditions. A total of 67 genes were identified as consistently associated with the elevated 85% or 100% ERH conditions and included fungal developmental regulators and secondary metabolite genes such as brlA (log2FC = 7.39, upregulated at 100% compared to 85%) and stcC (log2FC = 8.78, upregulated at 85% compared to 50%).</p><p><strong>Conclusions: </strong>Our results demonstrate that moisture conditions more strongly influence gene expression of indoor fungal communities compared to species presence. Identifying genes indicative of microbial growth under damp conditions will help develop robust monitoring techniques for indoor microbial exposures and improve understanding of how dampness and mold are linked to disease. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"231"},"PeriodicalIF":13.8,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623788","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":"Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases.","authors":"Alejandro Artacho, Cintya González-Torres, Nuria Gómez-Cebrián, Paula Moles-Poveda, Javier Pons, Nuria Jiménez, María Jinglei Casanova, Juan Montoro, Aitana Balaguer, Marta Villalba, Pedro Chorão, Leonor Puchades-Carrasco, Jaime Sanz, Carles Ubeda","doi":"10.1186/s40168-024-01948-0","DOIUrl":"10.1186/s40168-024-01948-0","url":null,"abstract":"<p><strong>Background: </strong>Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the most efficient therapeutic options available to cure many hematological malignancies. However, severe complications derived from this procedure, including graft-versus-host disease (GVHD) and infections, can limit its success and negatively impact survival. Previous studies have shown that alterations in the microbiome are associated with the development of allo-HSCT-derived complications. However, most studies relied on single techniques that can only analyze a unique aspect of the microbiome, which hinders our ability to understand how microbiome alterations drive allo-HSCT-associated diseases.</p><p><strong>Results: </strong>Here, we have applied multiple \"omic\" techniques (16S rRNA and shotgun sequencing, targeted and un-targeted metabolomics) in combination with machine learning approaches to define the most significant microbiome changes following allo-HSCT at multiple modalities (bacterial taxa, encoded functions, and derived metabolites). In addition, multivariate approaches were applied to study interactions among the various microbiome modalities (the interactome). Our results show that the microbiome of transplanted patients exhibits substantial changes in all studied modalities. These include depletion of beneficial microbes, mainly from the Clostridiales order, loss of their bacterial encoded functions required for the synthesis of key metabolites, and a reduction in metabolic end products such as short chain fatty acids (SCFAs). These changes were followed by an expansion of bacteria that frequently cause infections after allo-HSCT, including several Staphylococcus species, which benefit from the reduction of bacteriostatic SCFAs. Additionally, we found specific alterations in all microbiome modalities that distinguished those patients who subsequently developed GVHD, including depletion of anti-inflammatory commensals, protective reactive oxygen detoxifying enzymes, and immunoregulatory metabolites such as acetate or malonate. Moreover, extensive shifts in the homeostatic relationship between bacteria and their metabolic products (e.g., Faecalibacterium and butyrate) were detected mainly in patients who later developed GVHD.</p><p><strong>Conclusions: </strong>We have identified specific microbiome changes at different modalities (microbial taxa, their encoded genes, and synthetized metabolites) and at the interface between them (the interactome) that precede the development of complications associated with allo-HSCT. These identified microbial features provide novel targets for the design of microbiome-based strategies to prevent diseases associated with stem cell transplantation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"229"},"PeriodicalIF":4.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605275","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":"Medium-chain fatty acid triglycerides improve feed intake and oxidative stress of finishing bulls by regulating ghrelin concentration and gastrointestinal tract microorganisms and rumen metabolites.","authors":"Jiaming Luan, Xin Feng, Yunlong Du, Dongxu Yang, Chunyin Geng","doi":"10.1186/s40168-024-01946-2","DOIUrl":"10.1186/s40168-024-01946-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;As a feed additive, medium-chain fatty acids (MCFAs)/medium-chain fatty acid triglycerides (MCTs) have been used in ruminant production, but mostly added in the form of mixed esters. Studies have shown that MCTs may have a positive effect on feed intake or oxidative stress in animals, but it is unclear which MCT could play a role, and the mechanism has not been elucidated. In this study, the effects of individual MCT on growth performance, serum intake-related hormones, and oxidative stress indices in finishing bulls were investigated and further studied the effects of MCT supplementation on gastrointestinal tract bacteria and rumen fluid metabolomics.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Four ruminally fistulated Yanbian cattle (bulls) were selected in 4 × 4 Latin square designs and allocated to four treatment groups: a control group (CON) fed a basal diet (total mixed ration, TMR), three groups fed a basal diet supplemented with 60 g/bull/day glycerol monocaprylin (GMC, C8), glycerol monodecanoate (GMD, C10), and glycerol monolaurate (GML, C12), respectively. Compared with the CON group, GMD tended to increase the dry matter intake (DMI) of finishing bulls (P = 0.069). Compared with the CON group, GMD significantly increased the concentration of ghrelin O-acyl transferase (GOAT), total ghrelin (TG), acylated ghrelin (AG), and orexins (P &lt; 0.05) and significantly decreased the concentrations of hydrogen peroxide (H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;), malondialdehyde, reactive oxygen species (ROS), and lipopolysaccharides (LPS) in the serum of finishing bulls (P &lt; 0.05). Compared with the CON group, GMD and GML significantly increased the concentrations of total antioxidant capacity (T-AOC), catalase, glutathione peroxidase (GSH-PX), glutathione reductase (GR), and nitric oxide (NO) in the serum of finishing bulls (P &lt; 0.05). Compared with the CON group, there were 5, 14, and 6 significantly different bacteria in the rumen digesta in the C8, C10, and C12 groups, respectively; there were 3, 10, and 5 significantly different bacteria in the rumen fluid in the C8, C10, and C12 groups, respectively; and only one differential bacteria (genus level) in the feces among the four treatment groups. Compared with the CON group, there were 3, 14, and 15 significantly differential metabolites identified under positive ionization mode in the C8, C10, and C12 groups, respectively, while under negative ionization mode were 3, 11 and 14, respectively. Correlation analysis showed that there was a significant correlation between DMI, GOAT, AG, GSH-PX, LPS, gastrointestinal tract bacteria, and rumen fluid metabolites.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Our findings revealed that different types of MCTs have different application effects in ruminants. Among them, GMD may improve the feed intake of finishing bulls by stimulating the secretion of AG. GMD and GML may change gastrointestinal tract microorganisms and produce specific rumen metabolites t","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"230"},"PeriodicalIF":4.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605274","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":"MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.","authors":"Annabel Cansdale, James P J Chong","doi":"10.1186/s40168-024-01949-z","DOIUrl":"10.1186/s40168-024-01949-z","url":null,"abstract":"<p><strong>Background: </strong>Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.</p><p><strong>Results: </strong>To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.</p><p><strong>Conclusions: </strong>The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"226"},"PeriodicalIF":13.8,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569123","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}