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Understanding the environmental drivers of microbial H 2 metabolisms is crucial for evaluating the risks for geological hydrogen storage. This study investigates how mineralogy and temperature affect H 2 consumption kinetics and metabolic activity of a microbial consortium containing methanogens, homoacetogens and sulfate reducers, incubated at 25, 34 and 40 °C under H 2 /CO 2 (80/20, v/v; 2 bars) with different rock powders (basalt, calcite, gypsum, and sandstone). The presence of gypsum favors sulfate reduction over methanogenesis and homoacetogenesis, especially at 25 °C. Methanogenesis is dominant at 34 and 40 °C with all sulfate-free mineralogies. At 25 °C, homoacetogenic bacteria are favored over methanogens and acetate production varies with the mineralogy. This suggests interactions of the microbial community with the rock powders, which may serve as a surface to form biofilms. These metabolic shifts are associated with radical changes in microbial populations, highlighting that ecosystems plasticity towards H 2 also depends on the mineralogical composition of the reservoir. • Both temperature and mineralogy affect H 2 consumption kinetics. • Gypsum powder favors sulfate reduction over methanogenesis and homoacetogenesis. • Low temperature favors homoacetogenesis over methanogenesis. • Proportions of methanogenesis and homoacetogenesis vary with the substrate mineralogy. • Metabolic shifts are associated with radical changes in microbial populations. [ABSTRACT FROM AUTHOR]

Metatranscriptomics is a promising technique for the characterization of active members of microbial populations and their functions. Only a subset of the functional potential of the gut microbiota is expressed and many functions are transcribed only by few organisms when broadly present, but corresponding information for many other habitats is lacking. Transcriptional activity may predict bacterial growth and death; undertranscription relative to the DNA abundance indicates loss of the taxa, while overtranscription precedes future growth. Metatranscriptomics has revealed medically relevant expression signatures as exemplified by signatures associated with preterm labor and risk for developing asthma. Metatranscriptomics has in proof-of-concept studies provided a higher diagnostic yield than metagenomics for detecting infectious diseases, but results should be validated. Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification. [ABSTRACT FROM AUTHOR]

This research investigated the application of in-situ biological hydrogen methanation within a continuous stirred tank reactor (CSTR) system under mesophilic conditions, with sewage sludge used as the substrate. Two CSTRs with an effective capacity of 5 L were installed and loaded with inoculum sludge with a volatile solid (VS) concentration of 1.2–1.5 %. They were fed mixed waste sludge with an organic loading rate (OLR) of 1.5 g VS/L and an average sludge retention time (SRT) of 19 days under mesophilic conditions at 37 °C. One of the reactors operated as a control, while the other was injected with H 2 through a microceramic membrane diffuser with a H 2 :CO 2 ratio of 4:1. The results of this study revealed that the addition of H 2 and the recirculation of residual hydrogen in biogas led to a substantial increase in the production of methane from 157 L/kg VS to 275 L/kg VS. Increasing the methane content in biogas from 52 % to 78 % yielded an impressive 42.8 % higher methane production rate. Metataxonomic analysis of the microbial community via high-throughput sequencing techniques revealed that the dominant acetoclastic and hydrogenotrophic methanogens were Methanosaeta and Methanoregula , respectively, with greater abundances of both groups in the experimental bioreactor. The dynamics of their activity in both bioreactors were analyzed via qPCR, and the functional genes encoding methyl-coenzyme M reductase (mcrA gene) and hydrogenase Ni-Fe presented comparable changes between RI and RII. By optimizing key operational parameters and closely examining the dynamics of the microbial community, this approach can contribute significantly to sustainable bioenergy solutions while minimizing environmental impact. [Display omitted] • Study on in-situ hydrogen methanation in mesophilic CSTRs using sewage sludge as a substrate. • Methane yield increased by 75 %,from 157 to 275 L/kgVS, with CH 4 content rising from 52 % to 78 %. • H₂ addition and recirculation increased methane production by 42.8 %. • Methanosaeta and Methanoregula were dominant methanogens, linked to higher methane output. [ABSTRACT FROM AUTHOR]

Gills and gut are the two primary osmoregulatory organs in fish. Recently, studies have expanded beyond the osmoregulatory mechanisms of these organs to explore the microbiota communities inhabiting them. It is now known that microbial communities in both organs shift in response to osmotic stress. However, there are limited studies identifying the major contributors and co-occurrence among these microbiota in both organs under seawater and freshwater transfer conditions. The current data mining report performed a bioinformatics analysis on two previous published datasets from our group, aiming to provide insights into host-bacteria relationships under osmotic stress. We divided the samples into four groups: control seawater gills (LSW); control seawater gut (TSW); freshwater transfer gills (LFW); and freshwater transfer gut (TFW). Our results showed that LSW had higher diversities, richness, and evenness compared to TSW. However, both the LFW and LSW did not show any significant differences after the freshwater transfer experiment. We further applied co-occurrence network analysis and, for the first time, reported on the interactions of taxa shaping the community structure in these two organs. Moreover, we identified enriched ectoine biosynthesis in seawater samples, suggesting its potential role in seawater environments. Increased mRNA expression levels of Na + /K + -atpase , and cftr , were observed in gills after 6 h of ectoine treatment. These findings provide a foundation for future studies on host-bacteria interactions under osmotic stress. [Display omitted] • New microbiota data in gills and gut of medaka under osmotic stress • Microbiota in seawater gills exhibit higher diversities than in the gut. • LefSe cladogram analysis identified that the major contributors in gut are opportunistic pathogenic bacteria. • Co-occurrence network analysis identified hub taxa in the gills and gut under seawater and freshwater transfer conditions. • Ecotine induces mRNA expression levels of ion transporters in gills. [ABSTRACT FROM AUTHOR]

Citrus is the most cultivated fruit crop worldwide. The modern citrus industry needs new bioproducts to overcome phytopathological threats, tolerate stresses and increase yield and quality. Mutualistic microbes from roots significantly impact host physiology and health and are a potentially beneficial resource. The bacterial microbiome can be surveyed to select potentially host-beneficial microbes. To achieve this goal, a prevalent "core-citrus" bacterial microbiome was obtained by picking those operational taxonomic units (OTUs) shared among samples within and across two Citrus rootstock genotypes grown in the same soil for more than 20 years. A sub-selection of main OTUs from the defined "core-citrus" microbiome was made based on abundance, host-enriched versus bulk soil, and rhizosphere-indicator species. In parallel, an extensive census of the cultivable microbiota was performed to collect a large number of bacterial citrus isolates. Metataxonomic data were linked to cultured microbes, matching 16S rRNA gene sequences from bacterial isolates with those counterpart OTU reference sequences from the selected bacterial "core-citrus" microbiome. This approach allowed selection of potentially host-beneficial bacteria to mine for agricultural probiotics in future biotechnological applications required for the citrus industry. [Display omitted] • Bacterial citrus microbiomes described using uncultured and cultured approaches. • The untapped diversity of host-associated bacteria as a source of benefits. • A collection of potentially beneficial bacteria for citrus is now available. • These bacteria could provide future agricultural probiotics required for the citrus industry. [ABSTRACT FROM AUTHOR]

This study examines the impact of the complex microbiota from long-term fermented kimchi, used as a backslop, on fermentation dynamics. The fermentation was conducted with autoclaved (group A) and non-autoclaved (NA) starter cultures. Bacterial and fungal communities were analyzed with 16S rRNA gene V4 and ITS2 region, respectively, and metabolites were profiled using gas chromatography–mass spectrometry. In the group NA, Levilactobacillus dominated at 64.3 % by day 5, while Pediococcus reached 57.4 % by day 50. Principal coordinate analysis showed that bacterial communities in both the starter culture and samples of the group NA became similar by the end of the fermentation (day 100); however, no significant differences were found in fungal community. Principal component analysis revealed distinct metabolite profiles, explaining 68.7 % of variability on PC1, with each group clustered separately by day 100. These results suggest that inoculating with microbiota from long-term fermentation can rapidly produce foods with desirable characteristics. • Bacterial community in kimchi resembled that of starter culture after 100 days. • Pediococcus constituted 57.4 % of total ASVs on day 50 in non-autoclaved group. • Metabolite profiles formed distinctly separated clusters based on time points. [ABSTRACT FROM AUTHOR]

The MaPLE study was a randomized, controlled, crossover trial involving adults ≥60 y.o. (n = 51) living in a residential care facility during an 8-week polyphenol-rich (PR)-diet. Results from the MaPLE trial showed that the PR-diet reduced the intestinal permeability (IP) in older adults by inducing changes to gut microbiota (GM). The present work aimed at studying the changes in serum metabolome in the MaPLE trial, as a further necessary step to depict the complex crosstalk between dietary polyphenols, GM, and intestinal barrier. Serum metabolome was monitored using a semi-targeted UHPLC-MS/MS analysis. Metataxonomic analysis (16S rRNA gene profiling) of GM was performed on faecal samples. Clinical characteristics and serum levels of the IP marker zonulin were linked to GM and metabolomics data in a multi-omics network. Compared to the control diet, the PR-diet increased serum metabolites related to polyphenols and methylxanthine intake. Theobromine and methylxanthines, derived from cocoa and/or green tea, were positively correlated with butyrate-producing bacteria (the order Clostridiales and the genera Roseburia , Butyricicoccus and Faecalibacterium) and inversely with zonulin. A direct correlation between polyphenol metabolites hydroxyphenylpropionic acid-sulfate, 2-methylpyrogallol-sulfate and catechol-sulfate with Butyricicoccus was also observed, while hydroxyphenylpropionic acid-sulfate and 2-methylpyrogallol-sulfate negatively correlated with Methanobrevibacter. The multi-omics network indicated that participant's age, baseline zonulin levels, and changes in Porphyromonadaceae abundance were the main factors driving the effects of a PR-diet on zonulin. Overall, these results reveal the complex relationships among polyphenols consumption, intestinal permeability, and GM composition in older adults, and they may be important when setting personalized dietary interventions for older adults. ISRCTN10214981. [ABSTRACT FROM AUTHOR]

Conservation Agriculture has been the subject of numerous studies for decades. However, its impact on the soil microbial community has often been overlooked. Recent studies have shed light on the changes in soil bacterial composition resulting from modifications in tillage practices, particularly when compared to conventional tillage methods. However, there is a lack of soil microbial community analysis conducted under conservation tillage and rainfed conditions in the Mediterranean basin. A metataxonomic approach was employed to assess the influence of 19 years (2004–2022) of minimum tillage (MT) and no-till (NT) practices, along with crop rotation, on the soil bacterial community at upper layers (15 cm depth). This field study involved three different seasonal moments throughout the year. Results revealed that both sampling time and tillage management significantly influenced the structure of the bacterial community, whereas no effect was observed due to the crop. May showed a higher taxonomic diversity than July and December, showing differences in some o fthe most abundant phyla, such as Actinobacteria, Firmicutes and Proteobacteria. On the other hand, the long-term application of NT was found to lead to a significant decrease in bacterial diversity, with lower abundances of the phyla Chloroflexi, Gemmatimonadetes, and Armatimonadota, as well as an increase in k-strategist bacteria compared to MT. However, no significant effect on alpha diversity was observed as a result of tillage. no variations in phyla composition were observed attributable to crop, as the primary distinctions were identified among legume crops, which were associated with different sampling times. Therefore, our conclusion is that over this period, NT did not promote microbial diversity in the upper soil layers, despite notable shifts in bacterial composition occurring across seasonal time points in both tillage management systems. [Display omitted] • Sampling time is a critical factor in metataxonomic analysis of soils. • Tillage management has a significant effect on soil bacterial communities. • No-tillage significantly reduces soil bacterial diversity. • No-till practices promote the enrichment k-strategist taxa of bacteria. [ABSTRACT FROM AUTHOR]

The operational temperature and nature of the substrates are two critical parameters in shaping the functional microbiota and determining the biogas productivity of field-scale anaerobic digesters. Elucidating microbial ecological configurations and dynamics as a function of parametric (temperature, pH, substrate variability etc.) variations is pivotal for effective process management, improving the process stability and digestion efficiency of large field-scale anaerobic digesters. Seventeen field-scale digesters treating food waste leachate, municipal wastewater sludge (MWS), and manure at 10 different sites across the Republic of Korea were studied to assess how substrate variations, including co-digestion and seasonal variation, affect biogas productivity and the compositional dynamics of the digester microbiota. The 16S rRNA gene metataxonomics and predictive metabolic pathway profiling revealed significant differences in the phylogenetic composition of the microbiota between the digester types depending on the presence of MWS in the substrate (p < 0.005). A clear compositional divergence was observed between the MWS and non-MWS substrate groups, with a high prevalence of Firmicutes and versatile organic matter-degrading genera (Fastidiosipila , Acholeplasma , etc.) in the non-MWS digesters, resulting in a significantly high biogas yield (53.4 Nm3/t). Predictive metabolic pathway profiling demonstrated the importance of acetoclastic methanogenesis in all anaerobic digestion groups subjected to the study. The results of this study suggest that metataxonomics and microbiota dynamics are good indicators of the process stability and efficiency of field-scale digesters across the parametric variations of field anaerobic digester systems. • Microbiota dynamics in large field-scale AD of various substrates were assessed. • A significant microbiota variance was observed between MWS and FWL-fed digesters. • Microbial dynamics of FWL digester group reflect significantly high biogas yield. • FWL digesters had high METH-ACETATE-PWY (acetoclastic methanogenesis) activity. [ABSTRACT FROM AUTHOR]

Fermented sausages have a long tradition originating from Europe and they constitute a significant part of the Mediterranean diet. This kind of products has a specific microbiota that is typical of the region or area where they are produced. Therefore, in order to protect the traditional aspect of these products, it is essential to understand the microbial ecology during fermentation by studying the dynamic changes that occur and to select autochthonous starter cultures that can be used in the production. In this paper we summarize the state of the art concerning the selection and use of starter cultures and ecology aspects of naturally fermented sausages. We pay particular attention to the application of bacteriocinogenic strains as they could provide an additional tool in the prevention of foodborne pathogens as well as enhancing the competitiveness of the starter organisms. Microbial ecology of fermented sausages has been determined by traditional microbiological methods, but the introduction in food microbiology of new molecular techniques complements the studies carried out so far and allows scientists to overcome the limitations of traditional methods. Next Generation Sequencing (NGS) techniques represent a change in the way microbiologists address ecology and diversity in foods. Indeed the application of metataxonomics and metagenomics will permit a detailed understanding of microbial ecology. A thorough knowledge of the mechanisms behind the biological processes will enhance meat fermentation control and modulation to obtain products with desired organoleptic properties. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to examine changes to the microbiota composition and metabolic profiles of seven patients with recurrent Clostridium difficile infection (rCDI), following treatment with faecal microbiota transplant (FMT).Methods: 16S rDNA sequencing and 1H NMR were performed on faecal samples from the patients (pre-, post-FMT, and follow-up) and the associated donor samples. Sparse partial-least-square analysis was used to identify correlations between the two datasets.Results: The patients' microbiota post-FMT tended to shift towards the donor microbiota, specifically through proportional increases of Bacteroides, Blautia, and Ruminococcus, and proportional decreases of Enterococcus, Escherichia, and Klebsiella. However, although cured of infection, one patient, who suffers from chronic alcohol abuse, retained the compositional characteristics of the pre-FMT microbiota. Following FMT, increased levels of short-chain fatty acids, particularly butyrate and acetate, were observed in all patients. Sparse partial-least-square analysis confirmed a positive correlation between butyrate and Bacteroides, Blautia, and Ruminococcus, with a negative correlation between butyrate and Klebsiella and Enterococcus.Conclusions: Clear differences were observed in the microbiota composition and metabolic profiles between donors and rCDI patients, which were largely resolved in patients following FMT. Increased levels of butyrate appear to be a factor associated with resolution of rCDI. [ABSTRACT FROM AUTHOR]

Blastocystis sp., is an intestinal protist with a broad host range and a high prevalence in human populations worldwide, even in developed Western countries. The publication of conflicting evidence has divided the scientific community about the pathogenic role of this parasite. Even though, genetic studies on Blastocystis sp. revealed associations between genotypes and different pathogenic profiles. Conventionally, the detection of this parasite is based on microscopic or PCR methods, which offer meager or null performance in detecting mixed infections. In this work, we applied a metataxonomic NGS approach targeting the V4 region of the eukaryotic SSU-rRNA gene and classical phylogenetic methods. This approach allowed us to detect Blastocystis sp. in stool samples from infected children living in an urban setting in the city of Medellin attending the same daycare center. Phylogenetic analysis identified the subtypes present in the children as ST1, ST2, and ST3. Besides, mixed infections of subtypes ST1 + ST3 were spotted in 16% of the analyzed stool samples. • Blastocystis subtypes circulating in children from Medellin • Metataxonomic/phylogenetic methods allow the detection of Blastocystis mixed subtype infections • The most frequent Blastocystis subtypes found were ST1 and ST2 • Blastocystis subtypes mixed infections of ST1 and ST3 subtypes • Blastocystis DNA was detected in the waters in one of the main WWTP of Medellin [ABSTRACT FROM AUTHOR]

We conducted a randomized double-blind, placebocontrolled multicentric study to investigate the influence of a synbiotic fermented milk on the fecal microbiota composition of 30 adults with irritable bowel syndrome (IBS). The synbiotic product contained Lactobacillus acidophilus La-5, Bifidobacterium animalis ssp. lactis BB-12, Streptococcus thermophilus, and dietary fiber (90% inulin, 10% oligofructose), and a heat-treated fermented milk without probiotic bacteria or dietary fiber served as placebo. Stool samples were collected after a run-in period, a 4-wk consumption period, and a 1-wk follow-up period, and were subjected to realtime PCR and 16S rDNA profiling by next-generation sequencing. After 4 wk of synbiotic (11 subjects) or placebo (19 subjects) consumption, a greater increase in DNA specific for L. acidophilus La-5 and Bifidobacterium animalis ssp. lactis was detected in the feces of the synbiotic group compared with the placebo group by quantitative real-time PCR. After 1 wk of followup, the content of L. acidophilus La-5 and B. animalis ssp. lactis decreased to levels close to initial levels. No significant changes with time or differences between the groups were observed for Lactobacillus, Enterobacteriaceae, Bifidobacterium, or all bacteria. The presence of viable BB-12- and La-5-like bacteria in the feces resulting from the intake of synbiotic product was confirmed by random amplification of polymorphic DNA (RAPD)- PCR. At the end of consumption period, the feces of all subjects assigned to the synbiotic group contained viable bacteria with a BB-12-like RAPD profile, and after 1 wk of follow-up, BB-12-like bacteria remained in the feces of 87.5% of these subjects. The presence of La-5-like colonies was observed less frequently (37.5 and 25% of subjects, respectively). Next-generation sequencing of 16S rDNA amplicons revealed that only the percentage of sequences assigned to Strep. thermophilus was temporarily increased in both groups, whereas the global profile of the fecal microbiota of patients was not altered by consumption of the synbiotic or placebo. In conclusion, daily consumption of a synbiotic fermented milk had a short-term effect on the amount and proportion of La-5-like strains and B. animalis ssp. lactis in the fecal microbiome of IBS patients. Furthermore, both synbiotic and placebo products caused a temporary increase in fecal Strep. thermophilus. [ABSTRACT FROM AUTHOR]

Stone-built cultural heritage exposed to urban environment is a habitat where heterogeneous microbial communities grow, inducing significant biodeterioration. The conservation of the Cathedral of Santa Maria del Fiore in Florence is a main issue of worldwide concern. We previously investigated the dark discoloration of the external white marble and the associated microbiota in two study sites of Florence Cathedral, one northwest and the other southeast exposed, through microscopy and cultivation-dependent methods. The aim of this study was to obtain a more in-depth characterization of the microbial communities inhabiting marble in these two areas. Bacterial and fungal diversity was investigated through DNA metabarcoding of the 16S rRNA gene and ITS region, respectively. Furthermore, the metabolic activity of the entire microbial community was analyzed through Biolog™ Ecoplate technology, a tool rarely used in the investigation of biodeterioration. The taxonomic analysis evidenced a different structure of the communities in the two study sites. The Phenotype Microarray assay showed different metabolic profiles, with a higher metabolic potential of the southeast community. Cultivated bacteria showed the capacity for carbonate dissolution and precipitation. • The microbiota of darkened marble of Florence Cathedral was investigated. • The cultivated community showed CaCO 3 dissolution and re-mineralization potential. • Taxonomic structure of bacterial and fungal communities differs at the two study sites. • The south-east community showed a higher metabolic activity than the north-west one. • Phenotype Microarray is a useful tool to investigate epilithic communities' activity. [ABSTRACT FROM AUTHOR]

[Display omitted] • The genus Ethanoligenens was described as dominant for the first time in sugary Kefir. • Greater microbial diversity was observed in the sugary kefir beverage than in the grains. • Sugary kefir grains can be used as an inoculum to develop an isotonic beverage. The objective of this study was to apply for the first time sugary kefir to produce a new isotonic with low sodium. Additionally, the microbial community profile of grains and fermented kefir was evaluated through metataxonomics. The kefir grains were inoculated into filtered water containing 40 g L-1 sugar at 25 °C for 48 h. Grains and beverage samples were collected at 0, 24, and 48 h for DNA extraction. The grains were separated, and the beverage was used to prepare the isotonic. The isotonic consisted of kefir (85% v/v), pasteurized juice (15% v/v), sodium citrate (0.2 g L-1), sodium chloride (0.427 g L-1), maltodextrin (22 g L-1) and citric acid (0.7 g L-1). The physicochemical and microbiological parameters were performed on days 0, 7, 15, and 30. All isotonic obtained presented sodium content below the commercial control. The presence of lactic acid bacteria and yeasts in all periods evaluated demonstrated the viability of isotonic kefir. Through metataxonomy, the genus Ethanoligenens was described as dominant for the first time in sugary kefir. Furthermore, the microbial diversity in the beverage was higher than that observed in the grains. This study provided a new low sodium isotonic based on sugary kefir for the first time. [ABSTRACT FROM AUTHOR]

[Display omitted] • We study the impact of lactic acid bacteria (LAB) starters on microbial composition in kimchi fermentation. • Bacteriophages modulate bacterial communities associated with fermentation. • Microbial composition differences impacted the metabolites produced in kimchi. • LAB starters are an important factor contributing to fermented food quality. Lactic acid bacteria (LAB) in kimchi, a traditional Korean food, are major fermentative microorganisms affecting the quality, safety, and nutritional and organoleptic properties of the final product. In this study, we determined the role of three key LAB strains, Leuconostoc gelidum , Latilactobacillus sakei , Weissella koreensis originated from different raw ingredients during natural fermentation, as opposed to an axenic environment. Starter cultures were inoculated into food with wild indigenous microbial communities, and the dynamics of bacterial communities and metabolites were analyzed during fermentation. As bacteriophages within the food viral community directly affect fermentation by influencing bacterial function and composition, the diversity and composition of DNA viral communities were compared with those of corresponding bacterial communities using a metagenomic approach. Our results provide insights into the ecological role of LAB starters in food fermentation and the potential impact of bacteriophages as modulators of bacterial communities associated with the fermentation properties of kimchi. [ABSTRACT FROM AUTHOR]

[Display omitted] • Effects of main ingredient on vegetable food (kimchi) fermentation was investigated. • Changes of bacteria and metabolite profile by the main ingredient were analyzed. • The main ingredient affected the fermentation properties of the food. Kimchi is a fermented food prepared via spontaneous fermentation by lactic acid bacteria originating from raw ingredients. To investigate the effect of these ingredients on food fermentation, four types of food that differed only in their main raw ingredients (kimchi cabbage, green onion, leaf mustard, and young radish) were evaluated. The major microorganisms were Leuconostoc gelidum , Weissella kandleri , and Lactobacillus sakei groups. The distribution of these species depended on the sample type. All three species were primarily distributed in the food prepared from kimchi cabbage and young radish; however, the Lac. sakei group was hardly found in the food prepared using green onion and leaf mustard. Metabolite analysis results showed that the free sugar, organic acid, ethanol, and amino acid profiles differed with the sample type. This study indicates that the main ingredients could be an important factor in determining the composition of the microbial community and the metabolite composition. [ABSTRACT FROM AUTHOR]

• We investigated the origin source of fermentative microbes of kimchi. • The dominant fermentative microbial taxa differed according to the raw ingredients. • Not all ingredients carried the microbes capable of processing kimchi fermentation. • The origin-reflexed microbial community assembly led to distinct metabolic phenotypes. Fermented foods constitute hubs of microbial consortia differentially affecting nutritional and organoleptic properties, quality, and safety. Here we show the origin source of fermentative microbes and fermentation dynamics of kimchi. We partitioned microbiota by raw ingredient (kimchi cabbage, garlic, ginger, and red pepper) to render kimchi fermented by each source-originated microbe pool and applied multi-omics (metataxonomics and metabolomics), bacterial viability, and physiochemical analyses to longitudinally collected samples. Only kimchi cabbage- and garlic-derived microbial inoculums yielded successful kimchi fermentations. The dominant fermentative microbial taxa and subsequent metabolic outputs differed by raw ingredient type: the genus Leuconostoc , Weissella , and Lactobacillus for all non-sterilized ingredients, garlic, and kimchi cabbage, respectively. Gnotobiotic kimchi inoculated by mono-, di-, and tri- isolated fermentative microbe combinations further revealed W. koreensis -mediated reversible microbial metabolic outputs. The results suggest that the raw ingredient microbial habitat niches selectively affect microbial community assembly patterns and processes during kimchi fermentation. [ABSTRACT FROM AUTHOR]