Dynamics Of Microbiota Research Articles

Agricultural practices and ditch size drive microbial community assembly and mediate N- and P-transformation in multistage drainage networks of paddy fields: Insights from a large-scale irrigation district in eastern China

Agricultural drainage ditches (ADDs) are ubiquitous and regarded as active zones for biogeochemical reactions and microbe-mediated pollutant removal. However, little is known about the microbial distribution and community assembly in ADDs. Here, a typical large-scale irrigation district, including five orders of farmland drainage systems (namely field, sublateral, head, branch, and trunk ditches that could efficiently remove excess water from paddy fields to downstream water bodies), was selected to investigate the ecological processes of microbial communities and N- and P-transformation processes in multistage ditches. We found that scale effects drove distinct environmental gradients and microbial community dissimilarities and that the five ordered ditches were grouped into three clusters (field vs. sublateral vs. head, branch, and trunk ditches). Specifically, the microbial communities in the field ditches located adjacent to the paddy fields were strongly selected by agricultural fertilization and irrigation drainage, enriching salt-tolerant microbes with high nitrification and inorganic P solubilization capabilities. In comparison, the sublateral ditches showed the highest removal performance for total nitrogen (13.28–55.80%) and total phosphorus (9.06–65.07%) during the growth of rice, which was mainly attributed to the enrichment of versatile microbiota (e.g., C39, Nitrospira, and Novosphingobium) as a result of the increased stochastic processes driven by the low redox potential. Notably, the specific gene (i.e., hzsB) for anaerobic ammonium oxidation in sublateral ditches was 1–2 orders of magnitude higher than in adjacent ditches, further contributing to N loss. As field water was discharged into the large-sized head, branch, and trunk ditches, the nutrient levels decreased sharply. At the same time, deterministic processes gained more importance (∼82%), leading to the flourishing of Synechococcus and increasing the potential risk of eutrophication. Overall, the microbial communities in multistage ADDs were co-shaped by agricultural practices and ditch size, which further governed the N and P removal performance. These results provide unique insights into microbiota assembly patterns and dynamics in multistage ADDs and important ecological knowledge for controlling agricultural non-point source pollutants by managing of small-sized ditches.

Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery.

Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery. Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing. The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD. This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.

Composition, function, and timing: exploring the early-life gut microbiota in piglets for probiotic interventions

BackgroundThe establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous effects. However, the optimal timeframe for introducing probiotics to achieve this outcome remains uncertain.ResultsIn the context of this investigation, we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time points. Simultaneously, we gathered vaginal and fecal samples from 23 sows. Employing 16S rRNA gene and metagenomic sequencing methodologies, we conducted a comprehensive analysis of the fluctuation patterns in microbial composition, functional capacity, interaction networks, and colonization resistance within the gut microbiota of piglets. As the piglets progressed in age, discernible modifications in intestinal microbial diversity, composition, and function were observed. A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal piglets. By D21, the microbial interaction network displayed a more concise and efficient configuration, accompanied by enhanced colonization resistance relative to the other two time points. Moreover, we identified three strains of Ruminococcus sp. at D10 as potential candidates for improving piglets' weight gain during the weaning phase.ConclusionsThe findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet development. This investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.

Spatiotemporal dynamics of root exudates drive microbial adaptation mechanisms under day-night alterations in constructed wetlands

Root exudates, as plant-derived metabolites, play a pivotal role in shaping the assembly of rhizosphere microorganisms by acting as nutrients and signals. However, the spatial–temporal dynamics of root exudates remained unknown and thus also, if the dynamic changes in root exudates mediated the assembly of rhizosphere microorganisms. In this study, we conducted an in-depth assessment of root exudates, examining the composition and functional attributes of rhizosphere microorganisms, alongside the pollutant removal performance of constructed wetlands (CWs) under spatial–temporal conditions. Results suggested that nutrient-rich root exudates potentially facilitate the emergence of intricate and resilient microbial communities harboring a plethora of functional microorganisms under light conditions. The function prediction results indicated that the relative abundances of genes related to C and N transformation were enhanced under light conditions. Accordingly, increased microbial metabolic activity would enhance the pollutant removal performance in CWs. Remarkably, the removal efficiencies of COD (82.79 %), NH4+-N (76.72 %), TN (28.29 %), and NO3–-N (94.73 %) were enhanced under light conditions. Furthermore, a higher content of root exudates was discerned at the upper layer, leading to an enhancement in the carbon and nitrogen metabolisms of CWs. These findings emphasized root exudate-induced divergence in microbiota dynamics and pollutant removal in CWs, providing valuable mechanistic insights for the adaption of microbiota in response to spatial–temporal variation.

The Atlantic salmon microbiome infected with the sea louse Caligus rogercresseyi reveals tissue-specific functional dysbiosis

The microbiota plays functional roles in almost all living organisms, influencing metabolism, defense, and nutrition. Conventionally, parasitism is defined as a bipartite interaction between host and parasites, where both organisms display molecular responses mainly associated with the immune system. However, the microbial community is another relevant factor that can interact during the parasite infection in fish farming. Therefore, this study aimed to characterize the Atlantic salmon microbiota's dynamics, correlation, and functional potential in skin and gut tissues during the sea louse Caligus rogercresseyi parasitism. The findings showed that the parasitism reduced the alpha and beta diversity in infested salmon's microbiota. This reduction favored the tissue-specific occurrence of opportunistic bacterial pathogens. Notably, Photobacterium was identified primarily on the skin, and Vibrio was predominant in the gut microbiota of infested individuals. Cluster analysis of full-length 16S rRNA sequencing suggested that C. rogercresseyi could be a vector for transmitting Tenacibaculum and Vibrio species. Network analysis evidenced that parasitism also perturbs the correlation of the skin and gut microbiota, revealing fewer associations in infested individuals. Finally, a contrasting effect on the functional potential of the skin and gut microbiome was found. Herein, the parasitism increased the biosynthetic processes and reduced degradation pathways in the skin; meanwhile, the opposite trend was observed in the gut microbiome. Overall, our results evidenced that sea lice parasitism induces tissue-specific functional dysbiosis and provides novel evidence about the harmful effects of sea lice in salmon aquaculture.

Characterizing the dynamics of the rumen microbiota, its metabolites, and blood metabolites across reproductive stages in Small-tailed Han sheep

ABSTRACT Different reproductive stages of mammals involve complex biological processes, and the intestinal microbiota, as an endocrine organ or an “invisible organ,” is involved in the regulation of hormone levels, immune function, and metabolism. However, the effects of the rumen microbiota, its metabolites, and blood metabolites on the reproductive performance of ruminants remain unclear. This study revealed that the Prevotella abundance increased significantly during pregnancy ( P < 0.01); the Fibrobacter abundance increased significantly during lactation ( P < 0.05); and rumen microbial carbohydrate metabolism, glucose biosynthesis, and metabolic functions were significantly enriched during pregnancy ( P < 0.05). Microbial metabolic profile analysis showed that the differentially abundant microbial metabolites during pregnancy and lactation were mainly enriched in the biosynthesis of ubiquinone and other terpenoid quinones, and there was a certain correlation with the microbiota. Among them, sapindoside A was increased during pregnancy, nicotinamide riboside and β-cryptoxanthin were reduced during pregnancy, and L-tryptophan was significantly increased during lactation. In addition, the volatile fatty acid levels in lactation were significantly higher than those in non-pregnancy and pregnancy ( P < 0.05), and the NH 3 -N content during pregnancy was significantly higher than that during lactation and non-pregnancy ( P < 0.05). Moreover, there were differences in the serum metabolite levels at different reproductive stages, and similar metabolites existed when comparing the rumen metabolites, which were mainly enriched in arachidonic acid metabolism, vitamin B6 metabolism, and ABC transporter protein, resulting in significantly higher serum IgA and IgM levels during lactation than during non-pregnancy and pregnancy ( P < 0.05). IMPORTANCE Our study illustrates the succession of the rumen microbiota and its metabolites in Small-tailed Han sheep at different reproductive stages. Among them, Firmicutes and Prevotella , which are related to energy metabolism, increased in abundance during pregnancy, while Fibrobacter , a fiber-degrading bacterium, increased in abundance during lactation. At the same time, the microbial metabolic profile and serum metabolic profile characteristics of different reproductive stages were revealed, and some functional pathways and metabolites related to energy and immunity were found. This study provides a reference for the health management of ruminants during non-pregnancy, pregnancy, and lactation.

From microbiome composition to functional engineering, one step at a time.

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Host and environmental influences on the gut bacterial community of carabid beetles in distinct paddy fields

AbstractThe relationship between the gut bacterial communities of carabid beetles and their habitats holds implications for understanding ecological dynamics. This study examined the gut bacterial communities of two carabid beetle species, Chlaenius pallipes and Pheropsophus jessoensis, in terraced and flat paddy fields. Differences in gut bacterial communities were evident at the species level and were based on habitat. Specifically, P. jessoensis had a greater presence of Firmicutes and Proteobacteria in terraced fields but more Actinobacteria in flatland fields. In comparison, C. pallipes consistently showed high levels of Firmicutes in both habitats. These differences were reflected at class and genus levels, emphasizing the role of host specificity in shaping gut microbiota. Alpha diversity metrics indicated that P. jessoensis hosted a more diverse bacterial community than C. pallipes. Terraced fields, however, showed slightly reduced diversity in P. jessoensis, suggesting environmental effects on microbial populations. Beta diversity analysis using Bray–Curtis distances differentiated the bacterial communities of the two beetles. Multivariate analysis of variance reinforced these findings. Insights from the Sloan neutral model indicate that environmental factors predominantly influence bacterial community assembly through stochastic processes. Functionally, metabolism was highlighted, indicating the role of gut bacteria in beetle metabolic processes. Notably, energy metabolism varied between field types, revealing environmental effects on gut bacterial functions. This study offers in‐depth insights into interactions between host‐specific and environmental factors influencing gut bacterial communities of carabid beetles, contributing to a broader understanding of microbial ecology and the roles of environment and host in microbiota dynamics.

Longitudinal analysis of vaginal microbiota during IVF fresh embryo transfer and in early pregnancy.

Non-Lactobacillus-dominated vaginal microbiota has been associated with poor gynecologic health and complications during pregnancy. Lactobacilli and especially Lactobacillus crispatus associate with good reproductive health and dominate the microbiota during healthy pregnancy. We examined whether the composition of vaginal microbiota at the time of fresh embryo transfer (ET) has an impact on the success of in vitro fertilization (IVF) and whether vaginal microbiota changes from IVF-ET to early pregnancy within individuals. Vaginal swab samples were collected from subfertile women at the time of IVF-ET (n = 76) and at the eighth gestational week (n = 21) from those who achieved clinical pregnancy. The microbiota composition was analyzed using 16S rRNA gene amplicon sequencing. L. crispatus was more abundant among the 30 women who achieved clinical pregnancy (46.9% vs. 19.1%, q = 0.039) and the 26 women who had live birth (43.3% vs. 23.1%, q = 0.32) compared to those who did not. Lactobacilli, mainly L. crispatus (76.2%), dominated all early pregnancy samples. Microbiota remained the same, i.e., Lactobacillus-dominated type in 52% (11/21), shifted from one Lactobacillus-dominated type to another in 24% (5/21), or shifted from mixed community to Lactobacillus-dominated type in 24% (5/21) women, but never from Lactobacillus dominance to non-lactobacilli dominance. Our results emphasize the role of L. crispatus in the success of IVF-ET and in early pregnancy. During pregnancy, the microbiota shifted toward L. crispatus dominance even if it was undetectable before pregnancy, indicating that most women hold a reservoir of this beneficial Lactobacillus in their reproductive tract.IMPORTANCEInfertility is a global public health issue which leads many couples to seek fertility treatments, of which in vitro fertilization (IVF) is considered to be the most effective. Still, only about one-third of the women achieve live birth after the first IVF embryo transfer (IVF-ET). Factors affecting embryo implantation are poorly known, but the female reproductive tract microbiota may play a key role. Our study confirms the beneficial role of vaginal lactobacilli, especially Lactobacillus crispatus, in the probability of achieving clinical pregnancy and live birth following IVF-ET. Our findings regarding the intra-individual shift of vaginal microbiota between non-pregnancy and pregnancy states are novel and provide new information about the dynamics of microbiota in the early steps of human reproduction. These findings may help clinicians in their attempts to optimize the conditions for ET by microbiota screening or modulation and timing the ET when the microbiota is the most favorable.

Microbial modulation of hormone signaling, proteomic dynamics, and metabolomics in plant drought adaptation

AbstractThe symbiotic synergy between proteome shifts in plants and microbial colonization orchestrates adaptive responses. This thorough review delves into the less explored domain of proteomic and metabolomic changes triggered by drought stress, shedding light on how they are influenced by interactions with microbiota. Notably, microbial mediation at the crossroads of hormone signaling, proteomic and metabolomic dynamics in drought adaptation emerges as a crucial focal point. Understanding the regulatory mechanisms that orchestrate these complex interactions offers a holistic view of the molecular foundation underlying a plant's ability to endure water scarcity. The insights gained from this exploration hold the potential to reshape agricultural practices and enhance drought‐tolerance through microbiota‐mediated mechanisms, supported by proteomic and metabolomic insights. As this review seamlessly integrates the latest developments in understanding drought stress responses, microbiota dynamics, proteomics and metabolomic, it reveals the interconnected molecular basis that underlies these aspects. Specifically, the review emphasizes the crucial role of microbial mediation at the crossroads of hormone signaling, proteomic and metabolomic dynamics during drought adaptation. This enhanced understanding of the intricate interactions among these components presents new opportunities for envisioning sustainable agricultural approaches in the face of the escalating challenges presented by intensifying drought scenarios.

The effect of migratory beekeeping on Indian honey bee (Apis cerana indica) microbiota – a first report

Migratory beekeeping is a widely extended practice aimed at increasing the yield of honey and pollination services. Microbial symbionts that inhabit the honey bee’s gut are essential to their host’s food digestion, immunity, and gut protection. Throughout the honey bee life cycle and at several migratory sites, the taxonomic composition of the gut microbiota changes. However, it is yet unknown how significant changes in migratory locations, such as altered floral supply, parasitism and pathogen infestation, affect the dynamics of the gut microbiota. The goal of this study was to describe the Indian honey bee (Apis cerana indica) gut microbiome at different migratory sites of Puducherry and Tamil Nadu. Our results found that the core bacterial composition of the microbiota was consistent over different migratory sites. Despite this stability, our comparisons of the microbiota of honey bees from the same colony show that there are differences in composition at different migratory sites. Likewise, there is variation in relative abundance between microbiomes of different migratory sites. The four most dominant phyla were Proteobacteria followed by Bacteroidota, Actinobacteriota and Firmicutes. Most of the isolates belonged to families of Xanthomonadaceae, Orbaceae, Weeksellaceae, Bifidobacteriaceae, Rhizobiaceae, Neisseriaceae, Lactobacillaceae, Dysgonomonadaceae, Clostridiaceae and Enterococcaceae. However, several commensal bacteria that proliferate in the hive environment including members of Lactobacillaceae (Lactobacillus kunkeei), Bifidobacteriaceae, Orbaceae and Neisseriaceae were also identified and considered as beneficial gut inhabitants and involved in the maintenance of a healthy microbiota. This is the first report on bee gut microbiota from Puducherry and Tamil Nadu geographically situated at the southeast coast of India.

Intestinal Microbiotas and Alcoholic Hepatitis: Pathogenesis and Therapeutic Value.

Alcoholic hepatitis (AH) is a rapidly progressing and severe stage of alcoholic liver disease, presenting a grim prognosis. Extensive research has elucidated several underlying mechanisms that contribute to the development of AH, including metabolic alterations, immune stimulation, and intestinal dysbiosis. These pathological changes intricately intertwine during the progression of AH. Notably, recent studies have increasingly highlighted the pivotal role of alterations in the intestinal microbiota in the pathogenesis of AH. Consequently, future investigations should place significant emphasis on exploring the dynamics of intestinal microbiota. In this comprehensive review, we consolidate the primary causes of AH while underscoring the influence of gut microbes. Furthermore, by examining AH treatment strategies, we delineate the potential therapeutic value of interventions targeting the gut microbiota. Given the existing limitations in AH treatment options, we anticipate that this review will contribute to forthcoming research endeavors aimed at advancing AH treatment modalities.

Introduction to Vaginal Microbiota and its Relevance in Gynecological Health

This article provides an introductory exploration into the vaginal microbiota and its significance in maintaining gynecological health. The vaginal microbiota plays a crucial role in sustaining a balanced and harmonious vaginal ecosystem, influencing various aspects of reproductive well-being. By examining the composition and dynamics of the vaginal microbiota, this article highlights its impact on preventing dysbiosis and associated infections. A deeper understanding of the intricate interactions within the vaginal microbiota can pave the way for targeted therapeutic interventions aimed at promoting and preserving gynecological health.

Effect of Fermentation Scale on Microbiota Dynamics and Metabolic Functions for Indigo Reduction.

During indigo dyeing fermentation, indigo reduction for the solubilization of indigo particles occurs through the action of microbiota under anaerobic alkaline conditions. The original microbiota in the raw material (sukumo: composted indigo plant) should be appropriately converged toward the extracellular electron transfer (EET)-occurring microbiota by adjusting environmental factors for indigo reduction. The convergence mechanisms of microbiota, microbial physiological basis for indigo reduction, and microbiota led by different velocities in the decrease in redox potential (ORP) at different fermentation scales were analyzed. A rapid ORP decrease was realized in the big batch, excluding Actinomycetota effectively and dominating Alkalibacterium, which largely contributed to the effective indigo reduction. Functional analyses of the microbiota related to strong indigo reduction on approximately day 30 indicated that the carbohydrate metabolism, prokaryotic defense system, and gene regulatory functions are important. Because the major constituent in the big batch was Alkalibacterium pelagium, we attempted to identify genes related to EET in its genome. Each set of genes for flavin adenine dinucleotide (FAD) transportation to modify the flavin mononucleotide (FMN)-associated family, electron transfer from NADH to the FMN-associated family, and demethylmenaquinone (DMK) synthesis were identified in the genome sequence. The correlation between indigo intensity reduction and metabolic functions suggests that V/A-type H+/Na+-transporting ATPase and NAD(P)H-producing enzymes drive membrane transportations and energization in the EET system, respectively.

Gut microbiota of Pacific white shrimp (Litopenaeus vannamei) exhibits distinct responses to pathogenic and non-pathogenic Vibrio parahaemolyticus.

Acute hepatopancreatic necrosis disease (AHPND), a high-mortality-rate shrimp disease, is caused by specific Vibrio parahaemolyticus (Vp) strains with a plasmid encoding the PirABVp toxins. As a bacterial pathogen, the invasion of AHPND-causing Vp might impose pressure on commensal microbiota in the shrimp gut, while the relationship between the pathogenesis of AHPND and the dysbiosis of gut bacterial communities remains unclear. Here we explored the temporal changes of shrimp gut microbiota in response to AHPND-causing and non-AHPND-causing Vp strains, with the non-infected controls as a baseline of the shrimp gut microbiota. The diversity and composition of bacterial communities from 168 gut samples (covering three treatments at seven time points with eight individuals per set) were investigated using 16S rRNA gene metabarcoding with high-throughput sequencing. The results showed that (i) species diversity of gut bacterial communities declined in Vp-infected shrimp, independent of the strain pathogenicity; (ii) taxonomic compositions of gut bacterial communities were significantly different between shrimp infected by AHPND-causing and non-AHPND-causing Vp strains; (iii) short-term (within 6 hours) compositional shifts in the gut microbiota were found only in AHPND-causing Vp-infected shrimp; (iv) the gut microbiota of AHPND-causing Vp-infected shrimp was enriched with genera Photobacterium and Vibrio, with a decline in Candidatus Bacilliplasma; and (v) functional predictions suggested the loss of normal metabolism due to compositional shifts in the gut microbiota. Our work reveals distinct features of community dynamics in shrimp gut microbiota, associated with pathogenic versus non-pathogenic Vibrio infections, providing a new perspective of the pathogenesis of AHPND. IMPORTANCE Shrimp production is continually threatened by newly emerging diseases, such as AHPND, which is caused by specific Vp strains. Previous studies on the pathogenesis of AHPND have mainly focused on the histopathology and immune responses of the host. However, more attention needs to be paid to the gut microbiota, which acts as the first barrier to pathogen colonization. In this study, we revealed that shrimp gut microbiota responded differently to pathogenic and non-pathogenic Vp strains, with bacterial genera Photobacterium and Vibrio enriched in pathogenic Vp-infected shrimp, and Candidatus Bacilliplasma enriched in non-pathogenic Vp-infected shrimp. Moreover, functional predictions suggested that changes in taxonomic compositions would further affect normal metabolic functions, emphasizing the importance of sustaining an equilibrium in the gut microbiota. Several biomarkers associated with specific microbial taxa and functional pathways were identified in our data sets, which help predict the incidence of disease outcomes.

Feeding and water temperature modulate the potential activity of gut microbiota in greater amberjack juveniles (Seriola dumerili)

Gut microbial communities are highly dynamic and respond to factors such as diet and host metabolism. However, there is limited knowledge on changes in gut microbiota during the daily cycle. To investigate how interactions between feeding and water temperature affected the diurnal dynamics and activity of the microbiota, we analyzed the qualitative and quantitative composition in feces of the potentially active bacterial community along a day cycle in greater amberjack juveniles (Seriola dumerili). Bacterial density (based on qPCR of 16S rDNA) in feces was relatively stable along the day. In contrast bacterial activity (based on qPCR of 16S rRNA) increased during the period of active feeding, and was reduced to pre-feeding levels four hours after the last meal. The relative potential activity of the bacterial community in fish feces varied with postprandial time. At the phylum level there was a shift from a Spirochaetes-dominated community in the morning to increased potential activity of Proteobacteria after feeding. At lower taxonomic level, i.e. order, the bacterial community was dominated by Mycoplasmoidales, which relative potential activity was maintained throughout the day in all treatments. By contrast, for absolute potential bacterial activity at the order level there was a peak in potential activity of several bacterial orders at 6h after first feeding, with the most noticeable increase observed for Mycoplasmoidales. Results from the present work also indicated a close relation between the effect of water temperature and microbial dynamics. This is the first study assessing the quantitative and qualitative effects of water temperature and daily feeding rhythm on the gut microbiota dynamics in fish. Feeding was the main driver modulating bacterial activity, promoting a peak in bacterial activity 6h after first feeding. However, water temperature also modulated gut microbiota dynamics, with a marked effect on the time scale. In addition, results indicate that analysis of absolute bacterial potential activity provides a better resolution of metabolically active gut microbial community, since a change in the absolute activity of a single taxon can alter the relative activity of all taxa.

The Impact of HPP-Assisted Biocontrol Approach on the Bacterial Communities' Dynamics and Quality Parameters of a Fermented Meat Sausage Model.

Traditional foods are increasingly valued by consumers, whose attention and purchase willingness are highly influenced by other claims such as 'natural', 'sustainable', and 'clean label'. The purpose of the present study was to evaluate the impact of a novel non-thermal food processing method (i.e., HPP-assisted biocontrol combining mild high hydrostatic pressure, listeriophage Listex, and pediocin PA-1 producing Pediococcus acidilactici) on the succession of bacterial communities and quality of a fermented sausage model. A comparative analysis of instrumental color, texture, and lipid peroxidation revealed no significant differences (p > 0.05) in these quality parameters between non- and minimally processed fermented sausages throughout 60-day refrigerated storage (4 °C). The microbiota dynamics of biotreated and untreated fermented sausages were assessed by 16S rRNA next-generation sequencing, and the alpha and beta diversity analyses revealed no dissimilarity in the structure and composition of the bacterial communities over the analyzed period. The innovative multi-hurdle technology proposed herein holds valuable potential for the manufacture of traditional fermented sausages while preserving their unique intrinsic characteristics.

Insights into prokaryotic metataxonomics and predictive metabolic function in field-scale anaerobic digesters treating various organic wastes

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.

Mitigative and anti-inflammatory effects of Trichostatin A against radiation-induced gastrointestinal toxicity and gut microbiota alteration in mice

Purpose Radiation-induced gastrointestinal injury (RIGI) is a serious side effect of abdominal and pelvic radiotherapy, which often limits the treatment of gastrointestinal and gynaecological cancers. RIGI is also observed during accidental radiological or nuclear scenarios with no approved agents available till date to prevent or mitigate RIGI in humans. Trichostatin A (TSA), an epigenetic modulator, has been currently in clinical trials for cancer treatment and is also well known for its antibiotic and antifungal properties. Methods In this study, partial body (abdominal) irradiation mice model was used to investigate the mitigative effect of TSA against gastrointestinal toxicity caused by gamma radiation. Mice were checked for alterations in mean body weight, diarrheal incidence, disease activity index and survival against 15 Gy radiation. Structural abnormalities in intestine and changes in microbiota composition were studied by histopathology and 16S rRNA sequencing of fecal samples respectively. Immunoblotting and biochemical assays were performed to check protein nitrosylation, expression of inflammatory mediators, infiltration of inflammatory cells and changes in pro-inflammatory cytokine. Results TSA administration to C57Bl/6 mice improved radiation induced mean body weight loss, maintained better health score, reduced disease activity index and promoted survival. The 16S rRNA sequencing of fecal DNA demonstrated that TSA influenced the fecal microbiota dynamics with significant alterations in the Firmicutes/Bacteriodetes ratio. TSA effectively mitigated intestinal injury, down-regulated NF-κB, Cox-2, iNOS expression, inhibited PGE2 and protein nitrosylation levels in irradiated intestine. The upregulation of NLRP3-inflammasome complex and infiltrations of inflammatory cells in the inflamed intestine were also prevented by TSA. Subsequently, the myeloperoxidase activity in intestine alongwith serum IL-18 levels was found reduced. Conclusion These findings provide evidence that TSA inhibits inflammatory mediators, alleviates gut dysbiosis, and promotes structural restoration of the irradiated intestine. TSA, therefore, can be considered as a potential agent for mitigation of RIGI in humans.

Gut, oral, and nasopharyngeal microbiota dynamics in the clinical course of hospitalized infants with respiratory syncytial virus bronchiolitis.

Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis and hospitalization in infants worldwide. The nasopharyngeal microbiota has been suggested to play a role in influencing the clinical course of RSV bronchiolitis, and some evidence has been provided regarding oral and gut microbiota. However, most studies have focused on a single timepoint, and none has investigated all three ecosystems at once. Here, we simultaneously reconstructed the gut, oral and nasopharyngeal microbiota dynamics of 19 infants with RSV bronchiolitis in relation to the duration of hospitalization (more or less than 5 days). Fecal samples, oral swabs, and nasopharyngeal aspirates were collected at three timepoints (emergency room admission, discharge and six-month follow-up) and profiled by 16S rRNA amplicon sequencing. Interestingly, all ecosystems underwent rearrangements over time but with distinct configurations depending on the clinical course of bronchiolitis. In particular, infants hospitalized for longer showed early and persistent signatures of unhealthy microbiota in all ecosystems, i.e., an increased representation of pathobionts and a depletion of typical age-predicted commensals. Monitoring infant microbiota during RSV bronchiolitis and promptly reversing any dysbiotic features could be important for prognosis and long-term health.