Microbial succession in different years of pit mud from a distillery in Sichuan for Nong-xiang Baijiu fermentation.

Microbial community and succession of 5-, 20-, and 50-year pit mud (PM) were uncovered in this study. The results showed that Bacteroidetes, Firmicutes and Ascomycota were dominant phyla in these PM samples. Interestingly, most sequences could not be classified into fungal taxa at the genus level by UNITE Database, the diversity and richness of bacteria in these PMs were higher than that of fungi. It was noteworthy that both 20-year and 50-year PMs exhibited higher abundances of Caproiciproducens and Petrimonas when compared with 5-year PM. While higher proportions of Lactobacillus and Acinetobacter were observed in the 5-year PM. Furfermore, these PMs microbiota mainly involved biosynthesis, degradation, and generation of precursor metabolites, which contributed to carbon cycling of Nong-xiang Baijiu anaerobic fermentation. Taken together, lactic acid bacteria depletion and caproic acid bacteria accumulation might be an important succession trend of PM microbiota during the long-term fermentation of Chinese Nong-xiang Baijiu. Supplementary Information: The online version contains supplementary material available at 10.1007/s10068-024-01558-4.

The dynamic changes and correlations between biochemical properties, flavor and microbial community during fermentation of asparagus by-products.

Asparagus by-products are the promising resource that urgently need to be re-valorized. This study investigated the dynamic changes in physicochemical properties, organic acids, free amino acids, volatile flavor compounds, microbial succession, and their correlations during 7-day spontaneous fermentation of asparagus by-products. Dominant organic acids (lactic acid and acetic acid) and free amino acids (Ser, Glu, and Ala) increased with fermentation time, with lactic acid reaching 7.73 ± 0.05 mg/mL and Ser increasing 56-fold after 7 days. A total of 58 volatile flavor compounds were identified using headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPEM/GC-MS), with esters, alcohols and acids as the main volatile flavor compounds. Fourteen volatile flavor compounds had odor activity value >1. High-throughput sequencing showed Firmicutes and Proteobacteria as the main bacterial phyla, dominated by lactic acid bacteria (Levilactobacillus, Lactiplantibacillus, Weissella). Correlation analysis revealed that five bacterial genera (Levilactobacillus, Lactiplantibacillus, Enterobacter, Pediococcus and Acetobacter) were highly correlated with organic acids, free amino acids, and volatile flavor compounds, indicating their pivotal role in forming the characteristic flavor of fermented asparagus by-products (FAPS). This study provides new insights into the flavor and microbial profile of FAPS, offering a strategy for value-added processing and industrial production.

Microbial community succession and changes of volatile compounds in the fermentation process of bamboo shoots.

Sour bamboo shoots are a traditional fermented delicacy that has garnered appreciation both domestically and internationally. This study investigates the intricate dynamics of microbial communities and volatile flavor compounds primarily derived from salted and pickled bamboo shoots during the fermentation process of Phyllostachys purpurea (PP). The dynamics of microorganisms and volatile flavor compounds were thoroughly examined initially using conventional isolation and cultivation methods in conjunction with high-throughput sequencing (HTS), headspace solid-phase microextraction (HS-SPME), and gas chromatography-mass spectrometry (GC-MS). In addition, we analyzed the core microorganisms responsible for modulating the volatile flavor profile. Our findings revealed 60 volatile compounds, 14 of which were the predominant contributors to the aroma of fermented PP. This group primarily comprised alcohols, aldehydes, and olefins. Notably, our investigation identified Lactobacillus and Candida as the dominant microbial genera during the middle and late stages of fermentation. These two genera exert a significant influence on the formation of characteristic aromas. Furthermore, we discovered that acids, sugars, and proteins pivotally influence the succession of microorganisms. Specifically, acids and soluble sugars drove the transition of Lactococcus to Lactobacillus and Pediococcus, whereas soluble proteins facilitated fungal succession from Candida to Kazachstania and Issatchenkia. These insights shed light on the community structure and succession patterns of flavor compounds throughout the PP fermentation process. Ultimately, they provide a foundation for optimizing the fermentation process and ensuring quality control in the production of sour bamboo shoots.

Phosphorus resource partitioning underpins diversity patterns and assembly processes of microbial communities in plateau karst lakes.

Eutrophication triggered by internal phosphorus (P) poses a substantial threat to the biodiversity of organisms in freshwater ecosystems. However, little is known about the linkages between P resource partitioning and microbial succession, especially in karst sediments. Here, we studied the diversity patterns and assembly processes of bacterial and archaeal communities in sediment cores from two historically hyper-eutrophicated karst lakes, Hongfeng Lake and Aha Lake, and investigated the relative contribution of P fractions to them. Our null and neutral models consistently indicated that bacterial and archaeal community assembly was judged to be deterministic rather than stochastic. We found a monotonically decreasing pattern for bacterial Shannon diversity toward deep sediments in Aha Lake, but U- or hump-shaped patterns for archaea in Hongfeng and Aha Lakes. Intriguingly, the community dissimilarity Bray-Curtis of bacteria and archaea consistently increased with increasing depth distance, with slopes of 0.0080 and 0.0069 in Hongfeng Lake and 0.0078 and 0.0087 in Aha Lake, respectively. Such cross-taxon congruence was well-supported by equivalent ecological processes (i.e., environmental selection). For bacteria and archaea, Shannon diversity was primarily affected by the total P (TP) fractions such as the loosely adsorbed TP or calcium-bound TP and sediment TP. Their community composition was significantly (P < 0.05) affected by calcium-bound inorganic P (Pi), loosely adsorbed Pi and reductant-soluble Pi. Although sediment properties were important, bacterial and archaeal diversity or community composition were well-explained by the Pi fractions, with high direct or indirect effects. In particular, Pi fractions exhibited stronger effects on bacterial and archaeal characteristics than organic P fractions. Taken together, our study provides novel insights into the ecological importance of P resource partitioning to microbial succession, which has crucial implications for disentangling the biogeochemical processes of P cycling in aquatic ecosystems.

Temperature-dependent microbial mechanism and accumulation of volatile fatty acids in primary sludge pretreated with peroxymonosulfate.

For revealing the influence of temperature on volatile fatty acids (VFAs) generation from primary sludge (PS) during the anaerobic fermentation process facilitated by peroxymonosulfate (PMS), five fermentation groups (15, 25, 35, 45, and 55 °C) were designed. The results indicated that the production of VFAs (5148 mg COD/L) and acetic acid (2019 mg COD/L) reached their peaks at 45 °C. High-throughput sequencing technology disclosed that Firmicutes, Proteobacteria, and Actinobacteria was the dominant phyla, carbohydrate metabolism and membrane transport were the most vigorous at 45 °C. Additionally, higher temperature and PMS exhibit synergistic effects in promoting VFAs accumulation. This study unveiled the mechanism of the effect of the pretreatment of PS with PMS on the VFAs production, which established a theoretical foundation for the production of VFAs.

Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage.

BACKGROUND: Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. RESULTS: QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. CONCLUSION: The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms.

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

Study on the Correlations between Quality Indicators of Dry-Aged Beef and Microbial Succession during Fermentation.

Dry-aged beef has been long favored by people due to its unique flavor and taste. However, the inner relationship between its overall quality formation and microbial changes during dry aging has not yet received much attention and research. To deeply reveal the forming mechanism of the unique flavor and taste of dry-aged beef, correlations between its three main quality indicators, i.e., texture, free amino acids (FAAs), volatile flavor compounds (VFCs), and microbial succession were analyzed in this study. The results showed that Staphylococcus spp. and Macrococcus spp. were key strains that influenced the total quality of dry-aged beef and strongly correlated with chewiness, hardness, and sweet FAAs (Ala), providing beef with unique palatability and taste. Additionally, among VFCs, Staphylococcus spp. and Macrococcus spp. showed a strong correlation with octanal and heptanal, and meanwhile, those highly correlated with nonanal, pentanol, and oct-1-en-3-ol were Debaryomyces spp., Psychrobacter spp., and Brochothrix spp., respectively, providing beef with a unique flavor. Staphylococcus spp. was proposed to be the dominant genus for dry-aged beef. This study provides valuable reference for the understanding of the role of microorganisms involved in dry aging.

Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation.

The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.

Deciphering the influence of salinity stress on the biological aniline degradation system: Pollutants degradation performance and microbial response.

In order to evaluate the impact of salinity gradients on the aniline biodegradation system, six reactors at salinity concentrations (0%-5%) were established. The results presented the salinity except for 5% imposed negligible effects on aniline degradation performance. Nitrification had prominent resistance to salinity (0%-1.5%) while were significantly restrained when salinity increased. The total nitrogen (TN) removal efficiency of Z4 (1.5%) was 20.5% higher than Z1 (0%) during the stable operation phase. Moreover, high throughput sequencing analysis showed that halophilic bacterium, such as Halomonas, Rhodococcus, remained greater survival advantages in high salinity system. The substantial enrichment of Flavobacterium, Dokdonella, Paracoccus observed in Z4 ensured its excellent nitrogen removal performance. The close cooperation among dominant functional bacteria was strengthened when salt content was below 1.5% while exceeding 1.5% led to the collapse of metabolic capacity through integrating the toxicity of aniline and high osmotic pressure.

Changes in microbial community structure related to biodegradation of eelgrass (Zostera marina).

Seagrass meadows produce organic carbon and deposit it on the seabed through the decaying process. Microbial activity is closely related to the process of eelgrass death and collapse. We investigated the microbial community structure of eelgrass during the eelgrass decomposition process by using a microcosm containing raw seawater and excised eelgrass leaves collected from a Zostera marina bed in Futtsu, Chiba Prefecture, Japan. The fast-growing microbes (i.e., Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia) rapidly adhered to the eelgrass leaf surface and proliferated in the first two weeks but gradually decreased the relative abundance as the months moved on. On the other hand, the slow-growing microbes (i.e., Cytophagia, Anaerolineae, Thaumarchaeota, and Actinobacteria) became predominant over the eelgrass surface late in the culture experiment (120, 180 days). The fast-growing groups of Gammaproteobacteria and Flavobacteriia appear to be closely related to the initial decomposition of eelgrass, especially the rapid decomposition of leaf-derived biopolymers. Changes in nitrogen content due to the bacterial rapid consumption of readily degradable organic carbon induced changes in the community structure at the early stage of eelgrass decomposition. In addition, shifts in the C/N ratio were driven by microbial community changes during later decomposition phases.

Interwoven processes in fish development: microbial community succession and immune maturation.

Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.

Regulating effects of low salt dry-curing pre-treatment on microbiota, biochemical changes and flavour precursors of grass carp (Ctenopharyngodon idella) fillets during storage at 4 °C.

Low salt dry-curing (LSD), as a healthier pre-treatment for the preservation of fishery products, is a potential technique substitute for excessively salty curing. The regulatory effects of 2 % and 3 % LSD on the quality evolution through an intrinsic correlation between microbiota succession and flavour precursors of refrigerated grass carp fillets were investigated in this study. The results showed that the LSD pre-treatment was effective in promoting proteolysis, free amino acid and fatty acid metabolism with the microbiota succession and quality evolution. Compared with unpre-treated samples, the 3 % LSD pre-treatment effectively extended the shelf life by 10 days within the acceptable quality attributes. Not only did the LSD pre-treatment lead to catalytic microbiota succession and inhibitive spoilage substance production but it also improved the flavour precursors, which are taste-active amino acids and polyunsaturated fatty acids (PUFAs). Moreover, considerable correlations between quality attributes, taste-active amino acids, PUFAs and microbiota were obtained.

Niche differentiation in microbial communities with stable genomic traits over time in engineered systems.

Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.

Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment.

Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.

Magnetic biochar accelerates microbial succession and enhances assimilatory nitrate reduction during pig manure composting.

Biochar promotes microbial metabolic activities and reduces N2O on aerobic composting. However, the effects of magnetic biochar (MBC) on the microbial succession and N2O emissions during pig manure composting remain unclear. Herein, a 42-day composting experiment was conducted with five treatment regimes: pig manure without biochar (CK), 5 % pig manure-based biochar (5 % PBC), 2 % MBC (2 % MBC), 5 % MBC (5 % MBC) and 7.5 % MBC (7.5 % MBC)), to clarify the variation in functional microorganisms and genes associated with nitrogen and direct interspecies electron transfer via metagenomics. Fourier-transform infrared spectroscopy showed that MBC possessed more stable aromatic structures than pig manure-based biochar (PBC), indicating its greater potential for nitrous oxide reduction. MBC treatments were more effective in composting organic matter and improving the carbon/nitrogen ratio than PBC. The microbial composition during composting varied significantly, with the dominant phyla shifting from Firmicutes to Proteobacteria, Actinobacteria, and Bacteroidota. Network and hierarchical clustering analyses showed that the MBC treatment enhanced the interactions of dominant microbes (Proteobacteria and Bacteroidota) and accelerated the composting process. The biochar addition accelerated assimilatory nitrate reduction and slowed dissimilatory nitrate reduction and denitrification. The Mantel test demonstrated that magnetic biochar potentially helped regulate composting nutrients and affected functional nitrogen genes. These findings shed light on the role of MBC in mitigating greenhouse gas emissions during aerobic composting.

Microbial intervention improves pollutant removal and semi-liquid organo-mineral fertilizer production from olive mill wastewater sludge and rock phosphate.

Olive mill wastewater sludge (OMWS) represents a residual pollutant generated by the olive oil industry, often stored in exposed evaporation ponds, leading to contamination of nearby land and water resources. Despite its promising composition, the valorization of OMWS remains underexplored compared to olive mill wastewater (OMW). This study aims to identify potent native microbial species within OMWS suitable for bioremediation and its transformation into a high-value organic fertilizer. The microbial screening, based on assessing OMWS tolerance and phosphate solubilization properties in vitro, followed by a singular inoculation using a mixture of OMWS and rock phosphate (RP). Identification of FUN 06 (Galactomyces Geotrichum), a fungal species, employed as an inoculant in the treatment of sterile OMWS supplemented with RP. Results demonstrate that fungal inoculation notably diminished OMWS phytotoxicity while enhancing its physicochemical parameters, nutrient concentrations, and removal of toxic organic compounds by up to 90% compared to the control, and enhances plant growth, offering a sustainable approach to tackle environmental concerns. Additionally, metataxonomic analysis unveiled FUN 06's propensity to enhance the presence of microbial species engaged in pollutant degradation. However, higher RP dosage (10%) appeared to adversely affect bioprocess efficiency, suggesting a potential dose-related effect. Overall, FUN 06, isolated from OMWS evaporation ponds, shows promise for effective bioremediation and sustainable reuse. In fact, our results indicate that targeted microbial inoculation stands as an effective strategy for mitigating pollutants in OMWS, facilitating its conversion into a nutrient-rich organo-mineral fertilizer suitable for direct use, promoting its beneficial reuse in agriculture, thereby presenting a promising avenue for olive oil waste management.

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition.

BACKGROUND: The gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age. These maturational patterns have been well-characterized for bacteria, but limited descriptions exist for other microbiota members, such as fungi. Further, our current understanding of the prevalence of different patterns of bacterial and fungal microbiome maturation and how inter-kingdom dynamics influence early-life microbiome establishment is limited. RESULTS: We examined individual shifts in bacterial and fungal alpha diversity from 3 to 12 months of age in 100 infants from the CHILD Cohort Study. We identified divergent patterns of gut bacterial or fungal microbiome maturation in over 40% of infants, which were characterized by differences in community composition, inter-kingdom dynamics, and microbe-derived metabolites in urine, suggestive of alterations in the timing of ecosystem transitions. Known microbiome-modifying factors, such as formula feeding and delivery by C-section, were associated with atypical bacterial, but not fungal, microbiome maturation patterns. Instead, fungal microbiome maturation was influenced by prenatal exposure to artificially sweetened beverages and the bacterial microbiome, emphasizing the importance of inter-kingdom dynamics in early-life colonization patterns. CONCLUSIONS: These findings highlight the ecological and environmental factors underlying atypical patterns of microbiome maturation in infants, and the need to incorporate multi-kingdom and individual-level perspectives in microbiome research to improve our understandings of gut microbiome maturation patterns in early life and how they relate to host health. Video Abstract.

Microbiologic surveys for Baijiu fermentation are affected by experimental design.

The traditional Chinese alcoholic beverage Baijiu is produced by spontaneous fermentation of grains under anaerobic conditions. While numerous studies have used metagenomic technology to investigate the microbiome of Baijiu brewing, the microbial succession mechanism of Baijiu brewing has not been fully clarified, and metagenomic strategies for microecology surveys have not been comprehensively evaluated. Using the fermentation process of strong-flavor Baijiu as a model, we compared the data for bacterial communities based on short read 16S rRNA variable regions, V3-V4, and full-length 16S regions, V1-V9, to whole metagenomic shotgun sequencing (WMS) to measure the effect of technology selection on phylogenetic and functional profiles. The results showed differences in bacterial compositions and their relation to volatiles and physicochemical variables between sequencing methods. Furthermore, the percentage of V3-V4 sequences assigned to species level was higher than the percentage of V1-V9 sequences according to SILVA taxonomy, but lower according to NCBI taxonomy (P < 0.05). In both SILVA and NCBI taxonomies, the relative abundances of bacterial communities at both the genus and family levels were more positively correlated with WMS data in the V3-V4 dataset than in the V1-V9 dataset. The WMS identified changes in abundances of multiple metabolic pathways during fermentation (P < 0.05), including "starch and sucrose metabolism," "galactose metabolism," and "fatty acid biosynthesis." Although functional predictions derived from 16S data show similar patterns to WMS, most metabolic pathway changes are uncorrelated (P > 0.05). This study provided new technical and biological insights into Baijiu production that may assist in selection of methodologies for studies of fermentation systems.

Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making.

Microbial inoculation is an effective way to improve the quality of fermented foods via affecting the microbiota structure. However, it is unclear how the inoculation regulates the microbiota structure, and it is still difficult to directionally control the microbiota function via the inoculation. In this work, using the spontaneous fermentation of the starter (Daqu) for Chinese liquor fermentation as a case, we inoculated different microbiota groups at different time points in Daqu fermentation, and analyzed the effect of the inoculation on the final metabolic profile of Daqu. The inoculated microbiota and inoculated time points both significantly affected the final metabolites via regulating the microbial succession (P < 0.001), and multiple inoculations can promote deterministic assembly. Twenty-seven genera were identified to be related to microbial succession, and drove the variation of 121 metabolites. We then constructed an elastic network model to predict the profile of these 121 metabolites based on the abundances of 27 succession-related genera in Daqu fermentation. Procrustes analysis showed that the model could accurately predict the metabolic abundances (average Spearman correlation coefficients >0.3). This work revealed the effect of inoculation on the microbiota succession and the metabolic profile. The established predicted model of metabolic profile would be beneficial for directionally improving the food quality.IMPORTANCEThis work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality.