Microbiome最新文献

{"title":"A tale for two roles: Root-secreted methyl ferulate inhibits P. nicotianae and enriches the rhizosphere Bacillus against black shank disease in tobacco.","authors":"Siqi Ma, Qianru Chen, Yanfen Zheng, Tingting Ren, Rui He, Lirui Cheng, Ping Zou, Changliang Jing, Chengsheng Zhang, Yiqiang Li","doi":"10.1186/s40168-024-02008-3","DOIUrl":"10.1186/s40168-024-02008-3","url":null,"abstract":"<p><strong>Background: </strong>Root exudates serve as chemical signaling molecules that regulate rhizosphere interactions and control soil-borne diseases. The interactions between plants and the soil microbiome play dynamic and crucial roles in regulating the resistance of plants to biotic stress. However, the specific roles of many root exudates in plant pathogens remain unclear. The root exudate methyl ferulate, a naturally occurring and relatively non-toxic antifungal agent, has been applied to control postharvest pathogens and preserve foodstuffs and has not been used in plant disease control.</p><p><strong>Results: </strong>This study investigated the role of the root exudate methyl ferulate in controlling tobacco black shank disease. We observed that methyl ferulate was secreted in greater quantities in the tobacco resistant cultivar Gexin 3 following inoculation with P. nicotianae than in the susceptible cultivar Xiaohuangjin 1025. Our findings also revealed that methyl ferulate strongly inhibited P. nicotianae (EC₅₀ = 67.51 µg/mL), effectively controlling tobacco black shank disease by impairing NADH dehydrogenase function (the activity decreased by 50%). Furthermore, methyl ferulate recruited disease-suppressive rhizosphere microbes, such as Bacillus (the relative abundance of these microbes increases from 4.69% to 13.79%), thereby increasing disease resistance. The overexpression of caffeic acid O-methyltransferase NtCOMT10 resulted in increased methyl ferulate secretion (increased to 221.09% compared with that of the wild-type), concomitant improvement in the disease suppression of tobacco black shank disease (disease index decreased from 20% to less than 10%) and enrichment of beneficial microbes. In addition, methyl ferulate exerted antagonistic effects on other phytopathogens, such as B. cinerea, P. aphanidermatum, P. sojae, C. lagenarium and F. oxysporum.</p><p><strong>Conclusions: </strong>Our findings indicated that methyl ferulate, a component of root exudates regulated by NtCOMT10, can inhibit phytopathogens and enrich rhizosphere Bacillus against plant disease. The great dual effect of methyl ferulate on the control of phytopathogens and its low cost enable a novel potential avenue for controlling soil-borne fungal diseases. This study provides ingenious insights into controlling soil-borne diseases through beneficial root exudates. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"33"},"PeriodicalIF":13.8,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075008","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":"Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.","authors":"Dan Huang, Jingqiu Liao, Jose Luis Balcazar, Mao Ye, Ruonan Wu, Dongsheng Wang, Pedro J J Alvarez, Pingfeng Yu","doi":"10.1186/s40168-025-02030-z","DOIUrl":"10.1186/s40168-025-02030-z","url":null,"abstract":"<p><strong>Background: </strong>The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.</p><p><strong>Results: </strong>Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.</p><p><strong>Conclusions: </strong>Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"34"},"PeriodicalIF":13.8,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075010","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":"Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont.","authors":"Emma Marangon, Nils Rädecker, Joan Y Q Li, Marko Terzin, Patrick Buerger, Nicole S Webster, David G Bourne, Patrick W Laffy","doi":"10.1186/s40168-024-02006-5","DOIUrl":"10.1186/s40168-024-02006-5","url":null,"abstract":"<p><strong>Background: </strong>The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions between host, Symbiodiniaceae and prokaryotes, the mechanisms underlying the initial destabilization of these symbioses are poorly understood.</p><p><strong>Results: </strong>In a 2-month manipulative experiment, we exposed the coral Porites lutea to gradually increasing temperatures corresponding to 0-8 degree heating weeks (DHW) and assessed the response of the coral holobiont using coral and Symbiodiniaceae transcriptomics, microbial 16S rRNA gene sequencing and physiological measurements. From early stages of heat stress (< 1 DHW), the increase in metabolic turnover shifted the holobiont to a net heterotrophic state in which algal-derived nutrients were insufficient to meet host energy demands, resulting in reduced holobiont performance at 1 DHW. We postulate the altered nutrient cycling also affected the coral-associated microbial community, with the relative abundance of Endozoicomonas bacteria declining under increasing heat stress. Integration of holobiont stress responses correlated this decline to an increase in expression of a host ADP-ribosylation factor, suggesting that Symbiodiniaceae and Endozoicomonas may underlie similar endosymbiotic regulatory processes.</p><p><strong>Conclusions: </strong>The thermotolerance of coral holobionts therefore is influenced by the nutritional status of its members and their interactions, and this identified metabolic interdependency highlights the importance of applying an integrative approach to guide coral reef conservation efforts. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"31"},"PeriodicalIF":13.8,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074925","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":"Ningxiang pig-derived lactobacillus reuteri modulates host intramuscular fat deposition via branched-chain amino acid metabolism.","authors":"Mei Yang, Qian Xie, Jing Wang, Andong Zha, Jiashun Chen, Qian Jiang, Meng Kang, Qiuchun Deng, Yulong Yin, Bie Tan","doi":"10.1186/s40168-024-02013-6","DOIUrl":"10.1186/s40168-024-02013-6","url":null,"abstract":"<p><strong>Background: </strong>Gut microbiota has been extensively demonstrated to modulate host lipid metabolism. Higher intramuscular fat (IMF) accumulation in Chinese indigenous breed pigs is associated with their special gut microbiota structure. However, the specific microbes and metabolic pathways responsible for lipid deposition are still poorly understood.</p><p><strong>Results: </strong>In the present study, a comparative analysis of the gut microbiota and metabolome in obese Ningxiang (NX) pigs and lean Duroc × Landrace × Yorkshire (DLY) pigs was conducted. The results revealed a higher abundance of gut lactobacilli and a correlation of branched-chain amino acid (BCAA) metabolism pathway in NX pigs. We proceeded to verify the roles of various lactobacilli strains originating from NX pigs in BCAA metabolism and lipids deposition in SD rats. We demonstrated that L. reuteri is a fundamental species responsible for modulating lipid deposition in NX pigs and that increased circulating levels of BCAA are positively linked to greater lipid deposition. Additionally, it has been verified that L. reuteri originating from NX pigs has the ability to improve BCAA synthesis in the gut and enhance IMF content in lean DLY pigs. The expression of genes related to lipid synthesis was also significantly upregulated.</p><p><strong>Conclusions: </strong>Taken together, our results imply that NX pig-derived L. reuteri regulates BCAA metabolism and plays a potential role in improving the meat quality of lean pig breeds through modulation of host intramuscular lipid deposition. The results provide a new strategy for improving the meat quality of commercial pigs by influencing host metabolism through supplementing dietary additives. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"32"},"PeriodicalIF":13.8,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074929","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":"Gardnerella vaginalis-binding IgA in the urethra of sexually experienced males.","authors":"Rachel Liu, R M Galiwango, Daniel Park, Sanja Huibner, Maliha Aziz, Aggrey Anok, James Nnamutete, Yahaya Isbirye, John Bosco Wasswa, Deo Male, Godfrey Kigozi, Aaron A R Tobian, Jessica L Prodger, Cindy Liu, Bryan Coburn, Rupert Kaul","doi":"10.1186/s40168-024-02007-4","DOIUrl":"https://doi.org/10.1186/s40168-024-02007-4","url":null,"abstract":"<p><strong>Background: </strong>Genital inflammation increases HIV susceptibility and is associated with the density of pro-inflammatory anaerobes in the vagina and coronal sulcus. The penile urethra is a critical site of HIV acquisition, although correlates of urethral HIV acquisition are largely unknown. While Streptococcus mitis is a consistent component of the urethral flora, the presence of Gardnerella vaginalis has been linked with prior penile-vaginal sex and urethral inflammation. Here, we use a flow cytometry-based bacterial assay to quantify urethral IgA and IgG that bind G. vaginalis and S. mitis in a cross-sectional cohort of 45 uncircumcised Ugandan men and to evaluate their association with the urethral microbiome and local soluble immune factors.</p><p><strong>Results: </strong>Urethral antibodies binding both bacterial species were readily detectable, with G. vaginalis predominantly bound by IgA, and S. mitis equivalently by IgA and IgG. Gardnerella vaginalis-binding IgA was elevated in participants with detectable urethral Gardnerella, with the latter only present in participants who reported prior penile-vaginal sex. In contrast, detectable urethral S. mitis was not associated with sexual history or levels of S. mitis-binding IgA/IgG. The time from the last penile-vaginal sex was inversely correlated with the urethral concentrations of total IgA, G. vaginalis-binding IgA, and chemokines IL-8 and MIP-1β; these inflammatory chemokines were independently associated with higher total IgA concentration, but not with G. vaginalis-binding IgA.</p><p><strong>Conclusions: </strong>This first description of microbe-binding antibodies in the penile urethra suggests that urethral colonization by Gardnerella after penile-vaginal sex specifically induces a G. vaginalis-binding IgA response. Prospective studies of the host-microbe relationship in the urethra may have implications for the development of vaccines against sexually-transmitted bacteria. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"29"},"PeriodicalIF":13.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066547","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":"Impact of commercial gut health interventions on caecal metagenome and broiler performance.","authors":"Gladys Maria Pangga, Banaz Star-Shirko, Androniki Psifidi, Dong Xia, Nicolae Corcionivoschi, Carmel Kelly, Callie Hughes, Ursula Lavery, Anne Richmond, Umer Zeeshan Ijaz, Ozan Gundogdu","doi":"10.1186/s40168-024-02012-7","DOIUrl":"https://doi.org/10.1186/s40168-024-02012-7","url":null,"abstract":"<p><strong>Background: </strong>Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.</p><p><strong>Results: </strong>Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.</p><p><strong>Conclusions: </strong>All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"30"},"PeriodicalIF":13.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066553","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":"Reductive acetogenesis is a dominant process in the ruminant hindgut.","authors":"Qiushuang Li, Jiabin Huo, Gaofeng Ni, Fan Zhang, Shizhe Zhang, Xiumin Zhang, Rong Wang, Jinzhen Jiao, Zhongtang Yu, Xuanxuan Pu, Yipeng Yue, Emilio M Ungerfeld, Xiaoli Zhang, Jian Wu, Zhiliang Tan, Chris Greening, Min Wang","doi":"10.1186/s40168-024-02018-1","DOIUrl":"10.1186/s40168-024-02018-1","url":null,"abstract":"<p><strong>Background: </strong>The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.</p><p><strong>Results: </strong>To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H₂ production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.</p><p><strong>Conclusions: </strong>These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H₂ can be managed in accord to livestock methane mitigation efforts. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"28"},"PeriodicalIF":13.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059429","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":"The fungal microbiota modulate neonatal oxygen-induced lung injury.","authors":"Isaac Martin, Mary Silverberg, Ahmed Abdelgawad, Kosuke Tanaka, Brian A Halloran, Teodora Nicola, Erin D Myers, Jay P Desai, Catrina T White, Ibrahim Karabayir, Oguz Akbilgic, Laura Tipton, Samuel J Gentle, Namasivayam Ambalavanan, Brian M Peters, Luan D Vu, Viral G Jain, Charitharth V Lal, Stephania A Cormier, Joseph F Pierre, Tamás Jilling, Ajay J Talati, Kent A Willis","doi":"10.1186/s40168-025-02032-x","DOIUrl":"10.1186/s40168-025-02032-x","url":null,"abstract":"<p><strong>Background: </strong>The immature lungs of very preterm infants are exposed to supraphysiologic oxygen, contributing to bronchopulmonary dysplasia (BPD), a chronic lung disease that is the most common morbidity of prematurity. While the microbiota significantly influences neonatal health, the relationship between the intestinal microbiome, particularly micro-eukaryotic members such as fungi and yeast, and lung injury severity in newborns remains unknown.</p><p><strong>Results: </strong>Here, we show that the fungal microbiota modulates hyperoxia-induced lung injury severity in very low birth weight premature infants and preclinical pseudohumanized and altered fungal colonization mouse models. Instead of fungal communities dominated by Candida and Saccharomyces, the first stool microbiomes of infants who developed BPD had less interconnected community architectures with a greater diversity of rarer fungi. After using a pseudohumanized model to show that transfer to the neonatal microbiome from infants with BPD increased the severity of lung injury, we used gain and loss of function approaches to demonstrate that modulating the extent of initial neonatal fungal colonization affected the extent of BPD-like lung injury in mice. We also identified alterations in the murine intestinal microbiome and transcriptome associated with augmented lung injury.</p><p><strong>Conclusions: </strong>These findings demonstrate that features of the initial intestinal fungal microbiome are associated with the later development of BPD in premature neonates and exert a microbiome-driven effect that is transferable and modifiable in murine models, which suggests both causality and a potential therapeutic strategy. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"24"},"PeriodicalIF":13.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051888","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":"High-throughput analysis of microbiomes in a meat processing facility: are food processing facilities an establishment niche for persisting bacterial communities?","authors":"Zhaohui S Xu, Vi D Pham, Xianqin Yang, Michael G Gänzle","doi":"10.1186/s40168-024-02026-1","DOIUrl":"10.1186/s40168-024-02026-1","url":null,"abstract":"<p><strong>Background: </strong>Microbial spoilage in meat impedes the development of sustainable food systems. However, our understanding of the origin of spoilage microbes is limited. Here, we describe a detailed longitudinal study that assesses the microbial dynamics in a meat processing facility using high-throughput culture-dependent and culture-independent approaches to reveal the diversity, dispersal, persistence, and biofilm formation of spoilage-associated microbes.</p><p><strong>Results: </strong>Culture-dependent and culture-independent approaches revealed a large diversity of microbes within the meat facility, including 74 undescribed bacterial taxa and multiple spoilage-associated microbes. Ten out of 10 reconstituted microbial communities formed biofilms, and the biofilm biomass was generally higher at 4 °C than at 25 °C. Isolates obtained at different sampling times or from different sampling sites that differed in fewer than 10 genome-wide single-nucleotide polymorphisms were considered the same (persistent) strains. Strains of Carnobacterium maltaromaticum and Rahnella rivi persisted over a period of 6 months across sampling sites and time, stemming from floor drains in the cooler room. Meat isolates of Carnobacterium divergens, Rahnella inusitata, and Serratia proteamaculans originated from food contact and non-food contact environments of the packaging area.</p><p><strong>Conclusions: </strong>Culture-dependent isolation, complemented by culture-independent analyses, is essential to fully uncover the microbial diversity in food processing facilities. Microbial populations permanently resided within the meat processing facility, serving as a source of transmission of spoilage microbes. The ability of these microbes to coexist and form biofilms facilitates their persistence. Our data together with prior data on persistence of Listeria monocytogenes indicates that microbial persistence in food processing facilities is the rule rather than an exception. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"25"},"PeriodicalIF":13.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053005","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":"The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.","authors":"Chunxiao Wang, Yu Yang, Xiaoqing Xu, Dou Wang, Xianghui Shi, Lei Liu, Yu Deng, Liguan Li, Tong Zhang","doi":"10.1186/s40168-024-02009-2","DOIUrl":"10.1186/s40168-024-02009-2","url":null,"abstract":"<p><strong>Background: </strong>High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial composition (community structure) data are essential for environmental analytical microbiology, enabling characterization of community dynamics and assessing microbial pollutants for the development of intervention strategies. However, the relative abundances derived from sequencing impede comparisons across samples and studies.</p><p><strong>Results: </strong>This review systematically summarizes various absolute quantification (AQ) methods and their applications to obtain the absolute abundance of microbial cells and genetic elements. By critically comparing the strengths and limitations of AQ methods, we advocate the use of cellular internal standard-based high-throughput sequencing as an appropriate AQ approach for studying environmental microbiome originated from samples of complex matrices and high heterogeneity. To minimize ambiguity and facilitate cross-study comparisons, we outline essential reporting elements for technical considerations, and provide a checklist as a reference for environmental microbiome research.</p><p><strong>Conclusions: </strong>In summary, we propose absolute microbiome quantification using cellular internal standards for environmental analytical microbiology, and we anticipate that this approach will greatly benefit future studies. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"26"},"PeriodicalIF":13.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052451","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}