Complex Microbiome Research Articles

Comparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes

BackgroundLentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms.ResultCore genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L. parabuchneri strains screened.ConclusionThe findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.

Analysis of sputum microbial metagenome in COPD based on exacerbation frequency and lung function: a case control study

BackgroundThe role of the sputum microbiome in chronic obstructive pulmonary disease (COPD) progression remains elusive. As the advent of the new culture-independent microbial sequencing technique makes it possible to disclose the complex microbiome community of the respiratory tract. The aim of this study was to use metagenomic next-generation sequencing (mNGS) to confirm whether there are differences in sputum microbiome of COPD between different exacerbation frequencies and lung function.MethodsThirty-nine COPD patients were divided into a frequent exacerbators (FE) group (n = 20) and a non-frequent exacerbators (NFE) (n = 19) group according to their exacerbation history, or a mild group (FEV1/pre ≥ 50%, n = 20) and a severe group (FEV1/pre < 50%, n = 19) according to the lung function. Sputum was collected during their stable phase, followed by DNA extraction, untargeted metagenomic next-generation sequencing (mNGS) and bioinformatic analysis.ResultsmNGS identified 3355 bacteria, 71 viruses and 22 fungi at the specie level. It was found that Shannon index and Simpson index in FE group was lower than that in NFE group (p = 0.005, 0.008, respectively) but similar between mild and severe groups. Out of top 10 bacteria taxa, Veillonella, Fusobacterium and Prevotella jejuni had a higher abundance in NFE group, Rothia had a higher abundance in mild group. Linear discriminant analysis revealed that many bacterial taxa were more abundant in NFE group, and they mostly belonged to Actinobacteria, Bacteroidetes and Fusobacteria phyla. Frequency of exacerbations was also found to be negatively correlated with alpha diversity (with Shannon index, r = − 0.423, p = 0.009; with Simpson index, r = − 0.482, p = 0.002). No significant correlation was observed between alpha diversity and FEV1/pre.ConclusionsMicrobiome diversity in FE group was lower than that in NFE group. There was a significant difference in microbiome taxa abundance between FE and NFE groups, or mild and severe groups. These findings demonstrated that sputum microbiome community dysbiosis was associated with different exacerbation frequencies and lung function in stable COPD.

Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study.

Although high-throughput DNA sequencing-based methods have been of great value for determining the composition of microbial communities in various environments, there is the potential for inaccuracies arising from the sequencing of DNA from dead microorganisms. In this pilot study, we compared different sequencing-based methods to assess their relative accuracy with respect to distinguishing between viable and non-viable cells, using a live and heat-inactivated model community spiked into bovine milk. The methods used were shotgun metagenomics with and without propidium monoazide (PMA) treatment, RNA-based 16S rRNA sequencing and metatranscriptomics. The results showed that methods were generally accurate, though significant differences were found depending on the library types and sequencing technologies. Different molecular targets were the basis for variations in the results generated using different library types, while differences in the derived composition data from Oxford Nanopore Technologies-and Illumina-based sequencing likely reflect a combination of different sequencing depths, error rates and bioinformatics pipelines. Although PMA was successfully applied in this study, further optimisation is required before it can be applied in a more universal context for complex microbiomes. Overall, these methods show promise and represent another important step towards the ultimate establishment of approaches that can be applied to accurately identify live microorganisms in milk and other food niches.

Reshuffling of the Coral Microbiome during Dormancy.

Quiescence, or dormancy, is a response to stressful conditions in which an organism slows or halts physiological functioning. Although most species that undergo dormancy maintain complex microbiomes, there is little known about how dormancy influences and is influenced by the host's microbiome, including in the temperate coral Astrangia poculata. Northern populations of A. poculata undergo winter quiescence. Here, we characterized wild A. poculata microbiomes in a high-resolution sampling time series before, during, and after quiescence using 16S rRNA gene sequencing on active (RNA) and present (DNA) microbiomes. We observed a restructuring of the coral microbiome during quiescence that persisted after reemergence. Upon entering quiescence, corals shed copiotrophic microbes, including putative pathogens, suggesting a removal of these taxa as corals cease normal functioning. During and after quiescence, bacteria and archaea associated with nitrification were enriched, suggesting that the quiescent microbiome may replace essential functions through supplying nitrate to corals and/or microbes. Overall, this study demonstrates that key microbial groups related to quiescence in A. poculata may play a role in the onset or emergence from dormancy and long-term regulation of the microbiome composition. The predictability of dormancy in A. poculata provides an ideal natural manipulation system to further identify factors that regulate host-microbial associations. IMPORTANCE Using a high-resolution sampling time series, this study is the first to demonstrate a persistent microbial community shift with quiescence (dormancy) in a marine organism, the temperate coral Astrangia poculata. Furthermore, during this period of community turnover, there is a shedding of putative pathogens and copiotrophs and an enhancement of the ammonia-oxidizing bacteria (Nitrosococcales) and archaea ("Candidatus Nitrosopumilus"). Our results suggest that quiescence represents an important period during which the coral microbiome can reset, shedding opportunistic microbes and enriching for the reestablishment of beneficial associates, including those that may contribute nitrate while the coral animal is not actively feeding. We suggest that this work provides foundational understanding of the interplay of microbes and the host's dormancy response in marine organisms.

Stability of a dominant sponge-symbiont in spite of antibiotic-induced microbiome disturbance.

Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge-model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge-microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom-made, sterile, flow-through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic-resistant bacteria, resulting in more complex, but less specific bacteria-bacteria interactions than in untreated sponges. The abundance of the dominant symbiont, Candidatus Halichondribacter symbioticus, remained overall unchanged, reflecting its obligately symbiotic nature. Recolonization with the natural microbiome could not reverse antibiotic-induced dysbiosis. However, single bacterial taxa that were transferred, successfully recolonized the sponge and affected bacteria-bacteria interactions. By experimentally manipulating microbiome composition, we could show the stability of a sponge-symbiont clade despite microbiome dysbiosis. This study contributes to understanding both host-bacteria and bacteria-bacteria interactions in the sponge holobiont.

Novel trends of genome evolution in highly complex tropical sponge microbiomes

BackgroundTropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes—the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.ResultsA total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts’ molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.ConclusionsThese results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes.2qsxhK4E14RHhUQ45Lc7ZoVideo

Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis).

Simple SummaryThere are many microbial communities in the digestive tracts of animals, and the complex gut microbiome constitutes an intricate ecosystem and intestinal microbial community which has co-adapted with its host. The intestinal microecology plays an important role in the host’s maintenance of normal physical activities, such as substance metabolism, energy transmission, signal transduction, and the immune system. This study used high-throughput sequencing technology to sequence the fecal microbiota of sika deer (Cervus nippon) and wapiti (Cervus canadensis) in order to explore the composition of, and the similarity between, the fecal microbiota structures of sika deer and wapiti in the similar living environment. The species composition, relative abundance of fecal microbiota, alpha diversity, and differences in beta diversity were analyzed. The maintenance of the composition of the gut microbiota and a balanced intestinal environment through the diet plays a key role in maintaining the host’s health. The results demonstrate that the fecal microbiota of sika deer and wapiti share a similar fecal microbiota structure, but there was some evidence showing that the gut microbiota of these two animals exhibit a clear divergence at the species level.Microbial symbiotic associations may be beneficial, neutral, or harmful to the host. Symbionts exploit the host space and nutrition or use hosts as carriers to spread to other environments. In order to investigate the fecal bacterial communities of wild sika deer (Cervus nippon) and wapiti (Cervus canadensis), this study aimed to sequence and explore the composition of, and similarity between, the fecal microbiota of sika deer and wapiti using high-throughput sequencing. The composition and relative abundance of fecal microbiota, alpha diversity, and differences in beta diversity between the two species were analyzed. We found that no pathogenic bacteria were present in large quantities in the hosts. The dominant bacterial phyla found in the two deer species were similar and included Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes. Moreover, the deer also shared similar dominant genera, including the Rikenellaceae RC9 gut group, Ruminococcaceae_UCG-010, Ruminococcaceae_UCG-005, and Bacteroides. These results demonstrate that the sika deer and wapiti share a similar fecal microbiotal structure, probably due to their common diet and living environment, but there was some evidence of a difference at the species level. These analyses provide new insights into the health status of deer populations outside protected environments and offer a scientific framework for monitoring the health conditions of sika deer and wapiti.

Elucidation of Prebiotics, Probiotics, Postbiotics, and Target from Gut Microbiota to Alleviate Obesity via Network Pharmacology Study.

The metabolites produced by the gut microbiota have been reported as crucial agents against obesity; however, their key targets have not been revealed completely in complex microbiome systems. Hence, the aim of this study was to decipher promising prebiotics, probiotics, postbiotics, and more importantly, key target(s) via a network pharmacology approach. First, we retrieved the metabolites related to gut microbes from the gutMGene database. Then, we performed a meta-analysis to identify metabolite-related targets via the similarity ensemble approach (SEA) and SwissTargetPrediction (STP), and obesity-related targets were identified by DisGeNET and OMIM databases. After selecting the overlapping targets, we adopted topological analysis to identify core targets against obesity. Furthermore, we employed the integrated networks to microbiota–substrate–metabolite–target (MSMT) via R Package. Finally, we performed a molecular docking test (MDT) to verify the binding affinity between metabolite(s) and target(s) with the Autodock 1.5.6 tool. Based on holistic viewpoints, we performed a filtering step to discover the core targets through topological analysis. Then, we implemented protein–protein interaction (PPI) networks with 342 overlapping target, another subnetwork was constructed with the top 30% degree centrality (DC), and the final core networks were obtained after screening the top 30% betweenness centrality (BC). The final core targets were IL6, AKT1, and ALB. We showed that the three core targets interacted with three other components via the MSMT network in alleviating obesity, i.e., four microbiota, two substrates, and six metabolites. The MDT confirmed that equol (postbiotics) converted from isoflavone (prebiotics) via Lactobacillus paracasei JS1 (probiotics) can bind the most stably on IL6 (target) compared with the other four metabolites (3-indolepropionic acid, trimethylamine oxide, butyrate, and acetate). In this study, we demonstrated that the promising substate (prebiotics), microbe (probiotics), metabolite (postbiotics), and target are suitable for obsesity treatment, providing a microbiome basis for further research.

Conjunctival microbiota of newborns: Current state of the problem and clinical perspectives

The species composition of the conjunctival microbiota of newborns and first-year infants informs the selection of an optimal management tactics for the prevention of inflammatory responses. The effectiveness of antimicrobial therapy depends on the availability of susceptibility testing. The most common types of bacteria found in first-year infants include Firmicutes, Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes. These bacterium types are most sensitive to fluoroquinolones. The bacterial culture of neonates born naturally most frequently contain coagulase-negative staphylococci, Propionibacterium spp, and Corynebacterium spp., while that in neonates born by caesarean section feature coagulasenegative staphylococci, Propionibacterium spp, and Staphylococcus aureus. An examination of infants with neonatal dacryocystitis revealed a high incidence of inflammatory, fungal, and infectious diseases of the genital tract in their mothers. A correlation was established between the bacterial species obtained from conjunctival and cervicovaginal fluid samples. The microflora composition in older infants is characterized by higher complexity compared to that in younger infants. No significant environmental impact is observed in the group of infants under 6 months old. A more complex ocular surface microbiome in childhood is consistent with alterations in the gastrointestinal microbiome. No alterations in the ocular surface microbiome were observed in infants that underwent ophthalmic surgery. The abundance and composition of microflora was found to depend on the geographical location and individual specifics. The conducted research supports the development of a system for monitoring the conjunctival microbiota composition of newborns in obstetric and maternity hospitals.

S. boulardii Early Intervention Maintains Gut Microbiome Structure and Promotes Gut Mucosal Barrier Function in Early-Weaned Rats.

Early weaning leads to the disorder of the gut microbiome and gut mucosal barrier injury. Early intervention of gut microbiome colonization contributes to the development of the gut microbiome and gut function. The aim of this study was to explore the effects of Saccharomyces boulardii (S. boulardii) early intervention on the gut microbiome structure and gut mucosal barrier function of early-weaned rats. The results showed that S. boulardii early intervention improved growth performance along with a decrease in pathogenic bacteria, an increase in beneficial bacteria, a stable and complex microbiome, and a high level of microbial metabolism. Moreover, S. boulardii upregulated the mucosal barrier function including goblet cells and relative gene expression, tight junction, and sIgA level. Furthermore, S. boulardii suppressed the inflammatory response and promoted the anti-inflammatory response. Our study may provide a possible early intervention strategy for preventing an early weaning-induced disorder of the gut microbiome and loss of gut mucosal barrier function.

Contribution of omics to biopreservation: Toward food microbiome engineering.

Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.

Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori.

The complex gut microbiome is a malleable microbial community that can undergo remodeling in response to many factors, including the gut environment and microbial properties. Enterococcus has emerged as one of the predominant gut commensal bacterial and plays a fundamental role in the host physiology and health of the major economic agricultural insect, Bombyx mori. Although extensive research on gut structure and microbiome diversity has been carried out, how these microbial consortia are established in multifarious niches within the gut has not been well characterized to date. Here, an Enterococcus species that was stably associated with its host, the model organism B. mori, was identified in the larval gut. GFP–tagged E. faecalis LX10 was constructed as a model bacterium to track the colonization mechanism in the intestine of B. mori. The results revealed that the minimum and optimum colonization results were obtained by feeding at doses of 105 CFU/silkworm and 107 CFU/silkworm, respectively, as confirmed by bioassays and fluorescence-activated cell sorting analyses (FACS). Furthermore, a comprehensive genome-wide exploration of signal sequences provided insight into the relevant colonization properties of E. faecalis LX10. E. faecalis LX10 grew well under alkaline conditions and stably reduced the intestinal pH through lactic acid production. Additionally, the genomic features responsible for lactic acid fermentation were characterized. We further expressed and purified E. faecalis bacteriocin and found that it was particularly effective against other gut bacteria, including Enterococcus casselifavus, Enterococcus mundtii, Serratia marcescens, Bacillus amyloliquefaciens, and Escherichia coli. In addition, the successful colonization of E. faecalis LX10 led to drastically increased expression of all adhesion genes (znuA, lepB, hssA, adhE, EbpA, and Lap), defense genes (cspp, tagF, and esp), regulation gene (BfmRS), secretion gene (prkC) and immune evasion genes (patA and patB), while the expression of iron acquisition genes (ddpD and metN) was largely unchanged or decreased. This work establishes an unprecedented conceptual model for understanding B. mori–gut microbiota interactions in an ecological context. Moreover, these results shed light on the molecular mechanisms of gut microbiota proliferation and colonization in the intestinal tract of this insect.

Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants.

Soil microorganisms can colonize plant roots and assemble in communities engaged in symbiotic relationships with their host. Though the compositional dynamics of root-associated microbiomes have been extensively studied, the host transcriptional response to these communities is poorly understood. Here, we developed an experimental system by which rice plants grown under axenic conditions can acquire a defined endosphere microbiome. Using this setup, we performed a cross-sectional characterization of plant transcriptomes in the presence or absence of a complex microbial community. To account for compositional variation, plants were inoculated with soil-derived microbiomes harvested from three distinct agricultural sites. Soil microbiomes triggered a major shift in the transcriptional profiles of rice plants that included the downregulation of one-third to one-fourth of the families of leucine-rich repeat receptor-like kinases and nucleotide-binding leucine-rich repeat receptors expressed in roots. Though the expression of several genes was consistent across all soil sources, a large fraction of this response was differentially impacted by soil type. These results demonstrate the role of root microbiomes in sculpting the transcriptomes of host plants and highlight the potential involvement of the two main receptor families of the plant immune system in the recruitment and maintenance of an endosphere microbiome.

Exploring the Corn Microbiome: A Detailed Review on Current Knowledge, Techniques, and Future Directions

In their natural environment, plants are colonized by a plethora of microorganisms. These diverse microorganisms interact with each other and the host to form a complex microbiome community. A growing body of research suggests that the microbiome has a significant impact on plant yield or health by promoting growth, stress tolerance, and resistance to pathogens. Although plant microbiomes have great potential for improving plant health and productivity, studies on crop microbiomes, especially in corn, have only recently started to be conducted. During the last few years, progress in next-generation sequencing technologies has enabled an increasing number of studies of corn-associated microbiomes and their dynamics with the plant. The composition and differentiation of microbial communities are affected not only by environmental factors and agricultural management but also by host phenotype and genotype. Although challenges remain in understanding the microbiome, the combination of beneficial plant microbes, microbial community interactions, and the optimization of the taxonomic composition of microbiomes determine the overall health and fitness of the plant and thus lead to more sustainable agriculture. In this review, we present an overview of the current knowledge and research on corn microbiomes using traditional culture-based approaches and next-generation amplicon or metagenomic profiling, discuss results from these approaches with an emphasis on the influence of environmental and host genetic factors on corn-microbe interactions, and outline future directions and challenges in corn microbiome research. A better understanding of the corn microbiome diversity, function, and microbiology will contribute to the improvement of crop health and productivity. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Extension of PERMANOVA to Testing the Mediation Effect of the Microbiome.

Recently, we have seen a growing volume of evidence linking the microbiome and human diseases or clinical outcomes, as well as evidence linking the microbiome and environmental exposures. Now comes the time to assess whether the microbiome mediates the effects of exposures on the outcomes, which will enable researchers to develop interventions to modulate outcomes by modifying microbiome compositions. Use of distance matrices is a popular approach to analyzing complex microbiome data that are high-dimensional, sparse, and compositional. However, the existing distance-based methods for mediation analysis of microbiome data, MedTest and MODIMA, only work well in limited scenarios. PERMANOVA is currently the most commonly used distance-based method for testing microbiome associations. Using the idea of inverse regression, here we extend PERMANOVA to test microbiome-mediation effects by including both the exposure and the outcome as covariates and basing the test on the product of their F statistics. This extension of PERMANOVA, which we call PERMANOVA-med, naturally inherits all the flexible features of PERMANOVA, e.g., allowing adjustment of confounders, accommodating continuous, binary, and multivariate exposure and outcome variables including survival outcomes, and providing an omnibus test that combines the results from analyzing multiple distance matrices. Our extensive simulations indicated that PERMANOVA-med always controlled the type I error and had compelling power over MedTest and MODIMA. Frequently, MedTest had diminished power and MODIMA had inflated type I error. Using real data on melanoma immunotherapy response, we demonstrated the wide applicability of PERMANOVA-med through 16 different mediation analyses, only 6 of which could be performed by MedTest and 4 by MODIMA.

IMetaLab Suite: A one-stop toolset for metaproteomics.

Metaproteomics is a recently thriving technique that studies the collection of proteins in complex microbiomes of the human, animal, plant, and environment. The bioinformatics workflow required for metaproteomics research, from the database searchand protein quantification to downstream functional and taxonomic analysis has been challenging and thus limiting the accessibility of metaproteomics to microbiome researchers. To overcome these challenges, we have developed a set of tools named iMetaLab Suite. iMetaLab Suite includes the following components: (1) MetaLab Desktop, an automated database search software that facilities proteins identification and quantitation from microbiomes; (2) the automated iMetaReport that allows users to quickly access database search results and data set profiles; and (3) an interactive online toolset, iMetaShiny, covering most frequently used functional, taxonomic, and statistical analysis in metaproteomics. iMetaLab Suite is a free, easily accessible, and actively updated toolset available to assist researchers to explore metaproteomic data.

USING ULTRAVIOLET IRRADIATION TO DISINFECTCOMPOUND FEEDS

Compound feeds are sources of not only nutrients required to maintain animals’ vital activity, but also of a complex of microorganisms inhabiting them. This complex develops in them after the heat treatment of raw materials (extrusion, conditioning, expansion, etc.), which creates non-competitive conditions for the foreign microorganisms to enter (in particular, from non-grain and animal raw materials). At the same time, the animal's gastrointestinal tract contains its own complex microbiome, which in young animals (at the time of switching to pre-starter) is not yet fully formed and not very stable. It can be disturbed by foreign microbiota, which will lead to a decrease in productivity. In addition, the foreign microbiota requires an immune response from the body, which is a very energy-consuming process. Therefore, the disinfection of compound feed for young animals at the stage of production and in finished form is reasonable and important. The most promising method of disinfection today is ultraviolet irradiation, which is widely used for disinfection of surfaces, air and water. It is cheap, easy in mounting and maintenance and effective without disrupting any properties of the product or feed. For compound feeds, it is currently used only on livestock farms, and is not used on production lines. Therefore, the task of this study was to test the effectiveness of ultraviolet irradiation of a compound feed for further implementation in manufacture. Irradiation with a bactericidal lamp of a model feed mixture (60% crushed wheat, 30% sunflower oilcake, 10% wheat bran) was conducted. The numbers of MAFAnM (mesophilic aerobic and facultatively anaerobic microorganisms) declined from 1 million to 20 thousand cells per gram after 5 hours (300 minutes) of UVC exposition (254 nm wavelength). The diagram obtained coincides well with the reference diagram for a typical bacterial strain and shows that the use of ultraviolet irradiation is quite effective even without requiring a long-time exposition. Therefore, it can be used industrially to disinfect compound feeds and their raw materials.

Dietary Cholesterol‐Induced Gut Microbes Drive Nonalcoholic Fatty Liver Disease Pathogenesis in a Murine Model

Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are hepatic manifestations of metabolic syndrome and major indications for liver transplantation. Western diet contributes to disease pathogenesis, partially mediated through the gut microbiome, yet mechanisms remain elusive. Human epidemiological studies identified high dietary cholesterol intake as a NAFLD risk factor and it is essential to drive disease in murine models, yet little is known about its role in reshaping gut microbiota. Using the fast food (FF) diet murine model in germ‐free (GF) mice completely devoid of all microbes and their conventionally‐raised (control) counterparts harboring complex microbiomes, we hypothesized high dietary cholesterol‐induced gut microbiota impact NAFLD onset, progression, and severity.Male C57Bl/6 age‐matched GF and control mice were fed 1 of 4 semi‐purified diets: low‐fat (LF); high fat (HF); FF + 0.2% high cholesterol (FFHC); FF + 2% very high cholesterol (FFVHC) for 8 or 24 weeks. Fecal gut microbiota profiles were tracked over time via Illumina MiSeq 16S rRNA gene amplicon sequencing. Serum alanine transaminase (ALT) and lipopolysaccharide binding protein (LBP, an indicator of gut barrier function) were measured throughout the study. Livers were collected for histology and Illumina NovaSeq RNA‐sequencing.Despite equal caloric intake between GF and controls across diets, significant weight gain and increased liver weight to body weight ratios (P&lt;0.05) were observed only in control mice fed FF diets. GF mice were largely protected from disease, with no elevation in plasma ALT, LBP, or histology‐based NAFLD activity score (NAS) regardless of treatment. Conversely, FFVHC control mice exhibited significantly elevated plasma ALT after 8 weeks on diet, which was exacerbated at 24 weeks relative to LF control and all GF groups. FF diets significantly increased (FFHC: P&lt;0.05; FFVHC: P&lt;0.01) plasma LBP after 24 weeks. Control mice fed FF diets exhibited severe steatosis, where FFVHC significantly increased NAS at 8 (P&lt;0.05) and 24 (P&lt;0.001) weeks relative to LF control and all GF groups. Microbiota profiling revealed no change in α‐diversity regardless of diet in control mice. β‐diversity analysis showed HF and FF diets, particularly FFVHC, rapidly shifted gut microbiota community membership after only 4 weeks, preceding disease onset and was further exacerbated over time. Liver RNA‐seq revealed FFVHC diet in control, but not GF, mice significantly enriched genes involved in the KEGG pathway, “antigen processing and presentation” (Bonferroni P&lt;0.001) relative to HF‐fed counterparts at 24 weeks.Taken together, FF diet‐induced shifts in gut microbes are both a prerequisite for and precede NAFLD/NASH disease onset, which is exacerbated by increased dietary cholesterol, driving liver inflammation. These data provide unique insights into how Western diet components impact host‐microbe interactions in complex liver diseases, which may aid in identifying novel therapeutic interventions.

Stabilizing microbial communities by looped mass transfer

Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.