Dynamics Of Microbiota Research Articles

Effects of stressogenic factors on the course of metabolic-associated fatty liver disease. Review

Metabolic‑associated fatty liver disease (MAFLD) is one of the most widespread diseases worldwide, including Ukraine. The complex pathophysiological MAFLD mechanisms include the disturbances of various processes (insulin resistance, lipotoxicity, pro‑inflammatory activation, changes in intestinal microbiota (IM), etc.). MAFLD is closely associated with the mental disorders, and they potentiate the course of each other. Stress induces both behavioral and biological reactions, which activate all the hypothalamic–pituitary–adrenal axis, thus resulting in the rise in the levels of cortisol and proinflammatory biomarkers that may be involved in the MAFLD development. There is a lack of data related to the effects of the stressogenic factors of the wartime and postwar state on the formation and progression of MAFLD. Knowledge about the role of chronic stress biomarkers (dehydroepiandrosterone, prolactin, brain neurotropic factor (BDNF)) in the MAFLD pathogenesis is insufficient. The literature data regarding changes in the qualitative and quantitative composition of the intestinal microbiota at the level of the main phyla in MAFLD patients are contradictory. The dynamics of intestinal microbiota under the influence of stress factors of war and post‑war times is not investigated. Complex determination of the degree of violation of the intestinal epithelial barrier integrity, the state of the IM, the level of stress hormones and pro‑inflammatory factors in patients with MAFLD in the stressful conditions of war and post‑war state will make it possible to clarify the pathophysiological links of MAFLD formation and progression and to work out pathogenetically based prophylactic and therapeutic interventions to inhibit the development of inflammation and fibrosis processes in liver tissue in MAFLD patients by means of correction of the microbiota and modification of the stress factors of the war and post‑war state. Moreover, it will enable investigations of the effects of the developed therapy on the clinical manifestations, metabolic profile, IM composition, inflammation, and the level of neurotropic hormones in MAFLD patients. Thus, scientific research of the effects of stressogenic factors on the course of metabolic‑associated fatty liver disease and determination of its pathogenetic mechanisms is relevant and appropriate.

Ecological and dynamic analysis of gut microbiota in the early stage of azomethane-dextran sodium sulfate model in mice.

The success rate of azomethane-dextran sodium sulfate (AOM-DSS) model in mice has been a long-standing problem. Treatment of AOM and the first round DSS induces acute colitis and is of great significance for the success of AOM-DSS model. In this study, we focused on the role of gut microbiota in the early stage of AOM-DSS model. Few mice with obvious weight loss and high disease-activity score survived from double strike of AOM and the first round DSS. Different ecological dynamics of gut microbiota were observed in AOM-DSS treated mice. Pseudescherichia, Turicibacter, and Clostridium_XVIII were of significance in the model, uncontrolled proliferation of which accompanied with rapid deterioration and death of mice. Akkermansia and Ruthenibacterium were significantly enriched in the alive AOM-DSS treated mice. Decrease of Ligilactobacillus, Lactobacillus, and Limosilactobacillus were observed in AOM-DSS model, but significant drop of these genera could be lethal. Millionella was the only hub genus of gut microbiota network in dead mice, which indicated dysbiosis of the intestinal flora and fragility of microbial network. Our results will provide a better understanding for the role of gut microbiota in the early stage of AOM-DSS model and help improve the success rate of model construction.

Bacterial community mapping of the AIA mouse gastrointestinal tract under dietary intervention with skipjack tuna (Katsuwonus pelamis) elastin peptides

BackgroundOur previous study demonstrated that a dietary intervention with skipjack tuna (Katsuwonus pelamis) elastin peptides alleviated adjuvant-induced arthritis (AIA) and affected the gut microbiota of AIA mice. However, whether the faecal microbiota serves as a surrogate to reflect the dynamics of the gut microbiota has not been determined. MethodsUsing 16 S rRNA sequencing technology, the present study investigated the microbiota in three segments (stomach, colon and caecum) of mice to comprehensively define microbial dysregulation and regulation related to rheumatoid arthritis (RA). ResultsThe results showed that the composition and distribution of the microbiota in the stomach, colon and caecum were significantly different depending on their intrinsic environment and their functions, and the colon possessed the richest and most diverse microbiota structure. The gut microbiota of AIA mice showed ecological dysbiosis, and a dietary intervention with skipjack tuna elastin peptides improved this negative effect, particularly the changes in the gastric microbiota, which were most obvious at RA onset and remission. ImplicationThe results not only indicate the spatial heterogeneity of the gut microbiota in terms of composition and distribution, but also indicate the potential of the application of elastin peptides for the alleviation of RA.

Dynamic gut microbiota changes in patients with advanced malignancies experiencing secondary resistance to immune checkpoint inhibitors and immune-related adverse events.

Immune checkpoint inhibitors (ICIs) have been a breakthrough in cancer immunotherapy, but secondary resistance (SR) and immune-related adverse events (irAEs) are significant clinical dilemmas. Although the gut microbiota is associated with ICI efficacy and irAEs, the knowledge of longitudinal gut microbiota dynamics during SR and irAE development is still quite limited. This was a prospective observational cohort study of cancer patients initially receiving anti-programmed cell death-1 (PD-1) treatment between May 2020 and October 2022. Clinical information was collected to evaluate therapy response and AEs. Patients were divided into a secondary resistance (SR) group, a non-secondary resistance (NSR) group, and an irAE group. Fecal samples were longitudinally obtained from baseline across multiple timepoints and analyzed with 16S rRNA sequencing. Thirty-five patients were enrolled, and 29 were evaluable. After a median follow-up of 13.3 months, NSR patients had a favorable progression-free survival (PFS) compared with SR (457.9 IQR 241.0-674.0 days vs. 141.2 IQR 116.9-165.4 days, P=0.003) and irAE patients (457.9 IQR 241.0-674.0 days vs. 269.9, IQR 103.2-436.5 days, P=0.053). There were no significant differences in the microbiota between groups at baseline. Several previously reported beneficial microbiomes for ICI efficacy including Lachnospiraceae, Ruminococcaceae, Agathobacter, and Faecalibacterium showed decreasing trends as secondary resistance developed, yet not achieved significance (P>0.05). Significant changes in butyrate-producing bacteria were also presented in the SR cohort (P=0.043) with a decreasing trend upon secondary resistance occurrence (P=0.078). While the abundance of IgA-coated bacteria was stable in the SR cohort, there was a temporary decrease upon ICI treatment initiation and reestablishment after continuation of ICI treatment in the NSR cohort (primary ICI response: 0.06, IQR 0.04-0.10; durable ICI response: 0.11, IQR 0.07-0.14; P=0.042). Bacteroides contributed most to the difference between baseline and irAE occurrence, which decreased after irAE occurrence (Baseline: 0.10 IQR 0.07-0.36; irAE occurrence: 0.08 IQR 0.06-0.12) and was restored upon irAE remission to a comparable level as baseline (irAE remission: 0.10 IQR 0.09-0.18). The development of SR and irAEs is related to the longitudinal dynamics of the intestinal microbiota. The investigation into the preventative and protective effects of enteric microbe manipulation strategies is further required.

In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.

Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown. Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge. We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities. Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.

Dynamic changes in gut microbiota during pregnancy among Chinese women and influencing factors: A prospective cohort study.

Gut microbiota (GM) dynamics during pregnancy vary among different populations and are affected by many factors, such as living environments and diet. This study aims to observe and evaluate the changes in the structure and function of the GM from the first to the third trimester of pregnancy in Chinese women, and to explore the main factors affecting the changes in intestinal microecology. Fifty-five Chinese pregnant women were recruited for this study and their fecal samples were collected during the first (P1), second (P2), and third trimesters (P3) of pregnancy. We exploited metagenomic sequencing to compare the composition and function of the GM in different pregnancy periods. Bioinformatic analysis revealed that there were differences in the composition of the GM among P1, P2, and P3, as indicated by the increase in α-diversity and β-diversity of the GM and the differences in the relative abundances of distinct bacterial phyla. Gestational diabetes mellitus (GDM) was the main factor (P < 0.05) that affected the changes in GM at various stages of pregnancy. There were also disparities in the structure of the GM between the GDM group and non-GDM group in the P1, P2, and P3. The GDM group exhibited increased abundances in Ruminococcus_gnavus, Akkermansia_muciniphila, Alistipes_shahii, Blautia_obeum, and Roseburia_intestinalis; while, the abundances of Bacteroides coprocola, Bacteroides plebeius, Erysipelatoclostridium ramosum, and Prevotella copri were increased in the non-GDM group. Three of the four species enriched in the non-GDM group manifestied significantly negative correlations with the insulin-signaling pathway and lipopolysaccharide biosynthesis (r ≤ -0.3, adjusted P < 0.05). In the GDM group, Bacteroides vulgatus and Ruminococcus gnavus were significantly and positively correlated with insulin signaling pathway and lipopolysaccharide biosynthesis (r ≤ -0.3, adjusted P < 0.05) among the species enriched from early pregnancy. Virtually all of the species enriched in P2 and P3 were positively correlated with steroid hormone biosynthesis. These results suggest a potential role for the GM in the development of GDM, enabling the potential prevention of GDM by targeting the GM.

Occupational exposure in swine farm defines human skin and nasal microbiota.

Anthropogenic environments take an active part in shaping the human microbiome. Herein, we studied skin and nasal microbiota dynamics in response to the exposure in confined and controlled swine farms to decipher the impact of occupational exposure on microbiome formation. The microbiota of volunteers was longitudinally profiled in a 9-months survey, in which the volunteers underwent occupational exposure during 3-month internships in swine farms. By high-throughput sequencing, we showed that occupational exposure compositionally and functionally reshaped the volunteers' skin and nasal microbiota. The exposure in farm A reduced the microbial diversity of skin and nasal microbiota, whereas the microbiota of skin and nose increased after exposure in farm B. The exposure in different farms resulted in compositionally different microbial patterns, as the abundance of Actinobacteria sharply increased at expense of Firmicutes after exposure in farm A, yet Proteobacteria became the most predominant in the volunteers in farm B. The remodeled microbiota composition due to exposure in farm A appeared to stall and persist, whereas the microbiota of volunteers in farm B showed better resilience to revert to the pre-exposure state within 9 months after the exposure. Several metabolic pathways, for example, the styrene, aminobenzoate, and N-glycan biosynthesis, were significantly altered through our PICRUSt analysis, and notably, the function of beta-lactam resistance was predicted to enrich after exposure in farm A yet decrease in farm B. We proposed that the differently modified microbiota patterns might be coordinated by microbial and non-microbial factors in different swine farms, which were always environment-specific. This study highlights the active role of occupational exposure in defining the skin and nasal microbiota and sheds light on the dynamics of microbial patterns in response to environmental conversion.

Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model.

The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME®-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic.

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

Strengthening in microbiota dynamics and C, N, S transformation induced by novel synthesized pyrite/PHBV composites for advanced nitrogen and phosphate removal: Overlooked sulfate reduction process

Fine-grained pyrites are difficult to be denitrified under natural environment due to chemical oxidation with O2. In this study, the pyrite/PHBV composites were synthesized through high-temperature melting and realized nitrogen and phosphate removal under natural aerobic conditions. Results showed that pyrite/PHBV-40 composites had the highest denitrification rate of 0.61 mg NO3−–N /(L·h) with low SO42− production, and its removal efficiency of nitrogen and phosphorus was 98% and 41%, respectively. Microbial community structure analysis revealed that the enrich sulfate-reducing bacteria (SRB) on the pyrite/PHBV-40 composites demonstrated that the sulfate reduction driven by SRB enhanced denitrification process, and thereby the S cycle could underpin the potential self-sustainability of pyrite/PHBV-40 composites. Co-occurrence network analysis showed that Fe oxidizers/reducers (e.g., Ferruginibacter/Geobacter) and SRB (e.g., Desulfovibrio) were the keystone species in microbial community. Bugbase analysis showed that formed biofilms mainly consisted of aerobic and facultative anaerobic strains, which was corresponding to structure of biofilm including aerobic and anoxic layer. Partial mantel test revealed the total Fe and nutrients (e.g., N and P) are the drivers in OTU and phenotype composition, respectively. Metabolic pathway analysis suggested that pyrite/PHBV composites may not only accelerate glycolysis with rapid hydrolysis of PHBV, but also enhance the TCA cycle with high production of ATP and NADH. The final product of nitrate reduction is N2O or NO, and the cysJ gene play an important role in sulfate reduction in pyrite/PHBV systems. Overall, the novel synthesized pyrite/PHBV composites are an ideal functional material with high denitrification rate, no secondary pollution and long service life. Our study highlights pyrite/PHBV-induced strength in microbiota dynamics and C, N, S transformation, therein, the sulfate reduction process cannot be overlooked.

Dysbiosis of a microbiota–immune metasystem in critical illness is associated with nosocomial infections

Critically ill patients in intensive care units experience profound alterations of their gut microbiota that have been linked to a high risk of hospital-acquired (nosocomial) infections and adverse outcomes through unclear mechanisms. Abundant mouse and limited human data suggest that the gut microbiota can contribute to maintenance of systemic immune homeostasis, and that intestinal dysbiosis may lead to defects in immune defense against infections. Here we use integrated systems-level analyses of fecal microbiota dynamics in rectal swabs and single-cell profiling of systemic immune and inflammatory responses in a prospective longitudinal cohort study of critically ill patients to show that the gut microbiota and systemic immunity function as an integrated metasystem, where intestinal dysbiosis is coupled to impaired host defense and increased frequency of nosocomial infections. Longitudinal microbiota analysis by 16s rRNA gene sequencing of rectal swabs and single-cell profiling of blood using mass cytometry revealed that microbiota and immune dynamics during acute critical illness were highly interconnected and dominated by Enterobacteriaceae enrichment, dysregulated myeloid cell responses and amplified systemic inflammation, with a lesser impact on adaptive mechanisms of host defense. Intestinal Enterobacteriaceae enrichment was coupled with impaired innate antimicrobial effector responses, including hypofunctional and immature neutrophils and was associated with an increased risk of infections by various bacterial and fungal pathogens. Collectively, our findings suggest that dysbiosis of an interconnected metasystem between the gut microbiota and systemic immune response may drive impaired host defense and susceptibility to nosocomial infections in critical illness.

Community differentiation of rhizosphere microorganisms and their responses to environmental factors at different development stages of medicinal plant Glehnia littoralis.

Rhizosphere microorganisms play a key role in affecting plant quality and productivity through its interaction with plant root system. To figure out the bottleneck of the decline of yield and quality in the traditional Chinese medicinal herbs Glehnia littoralis they now encounter, it is important to study the dynamics of rhizosphere microbiota during the cultivation of G. littoralis. In the present study, the composition, diversity and function of rhizosphere microbes at different development stages of G. littoralis, as well as the correlation between rhizosphere microbes and environmental factors were systematically studied by high-throughput sequencing. There were significant differences between the rhizosphere microbes at early and middle-late development stages. More beneficial bacteria, such as Proteobacteria, and more symbiotic and saprophytic fungi were observed at the middle-late development stage of G. littoralis, while beneficial bacteria such as Actinobacteria and polytrophic transitional fungi were abundant at all development stages. The results of redundancy analysis show that eight environmental factors drive the changes of microflora at different development stages. pH, soil organic matter (SOM) and available phosphorus (AP) had important positive effects on the bacterial and fungal communities at the early development stage; saccharase (SC) and nitrate nitrogen (NN) showed significant positive effects on the bacterial and fungal communities at the middle and late stages; while urease (UE), available potassium (AK), and alkaline phosphatase (AKP) have different effects on bacterial and fungal communities at different development stages. Random forest analysis identified 47 bacterial markers and 22 fungal markers that could be used to distinguish G. littoralis at different development stages. Network analysis showed that the rhizosphere microbes formed a complex mutualistic symbiosis network, which is beneficial to the growth and development of G. littoralis. These results suggest that host development stage and environmental factors have profound influence on the composition, diversity, community structure and function of plant rhizosphere microorganisms. This study provides a reference for optimizing the cultivation of G. littoralis.

Multi-factor correlation analysis of the effect of root-promoting practices on tobacco rhizosphere microecology in growth stages

Some agronomic practices not only promote the development of crop roots and increase overall plant performance but also affect colonisation by rhizosphere microorganisms. However, the composition and temporal dynamics of the tobacco rhizosphere microbiota under different root-promoting practices are poorly understood. Here, we characterised the tobacco rhizosphere microbiota at the knee-high, vigorous growing, and maturity stages under the application of potassium fulvic acid (PFA), γ-Polyglutamic acid (PGA), soymilk root irrigation (SRI), and conventional fertilization (CK) and its correlation with root characteristics and soil nutrients. The results showed that three root-promoting practices notably improved the dry and fresh root weights. Total nitrogen and phosphorus, available phosphorus and potassium, and organic matter contents in the rhizosphere markedly increased at the vigorous growing stage. The rhizosphere microbiota was changed through root-promoting practices. However, with tobacco growth, the change of rhizosphere microbiota showed a pattern of slow first and then fast and the microbiota of different treatments gradually approached. SRI reduced plant-pathogenic fungi but increased chemoheterotrophic and phototrophic bacteria, and arbuscular mycorrhizal fungi. PFA and PGA markedly increased arbuscular mycorrhizal and ectomycorrhizal fungi at the knee-high stage, which benefitted tobacco nutrient absorption. The correlation between rhizosphere microorganisms and environmental factors varied at different growth stages. Notably, the rhizosphere microbiota was more sensitive to environmental factors at the vigorous growing stage, and the interactions were more complex than in other stages. Furthermore, a variance partitioning analysis showed that the influence of root–soil interaction on the rhizosphere microbiota increased with tobacco growth. Overall, all three root-promoting practices could improve root characteristics, rhizosphere nutrient, and rhizosphere microbiota to varying degrees and increase the tobacco biomass, among which PGA had the most obvious effect and most suitable for tobacco cultivation. Our findings revealed the role of root-promoting practices in shaping the rhizosphere microbiota during plant growth and elucidated the assembly patterns and environmental drivers of crop rhizosphere microbiota driven by the application of root-promoting practices in agricultural production.

Upper respiratory tract microbiota dynamics following COVID-19 in adults.

To date, little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, on the upper respiratory tract (URT) microbiota over time. To fill this knowledge gap, we used 16S ribosomal RNA gene sequencing to characterize the URT microbiota in 48 adults, including (1) 24 participants with mild-to-moderate COVID-19 who had serial mid-turbinate swabs collected up to 21 days after enrolment and (2) 24 asymptomatic, uninfected controls who had mid-turbinate swabs collected at enrolment only. To compare the URT microbiota between groups in a comprehensive manner, different types of statistical analyses that are frequently employed in microbial ecology were used, including ⍺-diversity, β-diversity and differential abundance analyses. Final statistical models included age, sex and the presence of at least one comorbidity as covariates. The median age of all participants was 34.00 (interquartile range=28.75-46.50) years. In comparison to samples from controls, those from participants with COVID-19 had a lower observed species index at day 21 (linear regression coefficient=-13.30; 95 % CI=-21.72 to -4.88; q=0.02). In addition, the Jaccard index was significantly different between samples from participants with COVID-19 and those from controls at all study time points (PERMANOVA q<0.05 for all comparisons). The abundance of three amplicon sequence variants (ASVs) (one Corynebacterium ASV, Frederiksenia canicola, and one Lactobacillus ASV) were decreased in samples from participants with COVID-19 at all seven study time points, whereas the abundance of one ASV (from the family Neisseriaceae) was increased in samples from participants with COVID-19 at five (71.43 %) of the seven study time points. Our results suggest that mild-to-moderate COVID-19 can lead to alterations of the URT microbiota that persist for several weeks after the initial infection.

Dynamics of bacterial community in the foregut and hindgut of earthworms with the nutrition supplied by kitchen waste during vermicomposting

Earthworm gut microbiota is vital in degrading bio-waste during vermicomposting. However, microbial dynamics in earthworm gut during this process are unclear. Thus, the aim is to firstly report the bacterial dynamics in both foregut and hindgut of earthworms over a 28 days’ timeframe of vermicomposting by Eisenia foetida with the nutrition supplied by kitchen waste. Results showed that except the changing of the bacterial diversity, composition and structure, dynamics of the foregut and hindgut bacteria also differed during vermicomposting which related to the changes of nutrient provision. Day 3 was a turning point. The abundant bacteria of the top 20 % genera nearly did not overlap between the foregut and hindgut. In the end of vermicomposting, a remarkable stable bacterial structure appeared in the hindgut compared to somewhat muddled one in the foregut. Understanding the dynamics of earthworm gut microbiota enables the improvements to regulate the efficiency of organic waste vermicomposting.

Characterization of rhizosphere bacterial microbiota under Robinia pseudoacacia plantations during long-term vegetation restoration on ex-arable land

Rhizosphere microbiota are intimately linked with plant growth and defense, but the microbial response to long-term vegetation restoration remains unclear. Here, soil samples were collected from Robinia pseudoacacia stands of different ages (7–35 years old) and a wheat field (control) for a comparative study of rhizosphere bacterial microbiota. The potential influencing factors were identified using principal coordinate analysis, partial least squares discriminant analysis, and partial least squares path modeling. Afforestation influenced soil environmental conditions and bacterial microbiome structure. Microbiota differentiation was mainly explained by niche compartments at the horizontal level. Age-related differences in the rhizosphere microbiota were not prominent, whereas soil samples of different niche compartments were clustered separately. The rhizosphere microbiota exhibited remarkable convergence with increasing stand age. The rhizosphere microbiota dynamics were inconsistent with those of the bulk soil microbiota. Soil organic carbon and available phosphorus contents were the major environmental factors influencing rhizosphere bacterial richness. Accordingly, rhizosphere niche predominantly drove microbiota differentiation along horizontal gradients depending on the soil environment. Growth of R. pseudoacacia trees played a non-significant role in the structuring of rhizosphere microbiota in the restored ecosystem. Results of this study enable a broader understanding of how rhizosphere microbiota respond to long-term afforestation, which could facilitate vegetation restoration.

Clustered covariation and spatial heterogeneity of mucosal microbiota dynamics during colorectal cancer progression

Clustered covariation and spatial heterogeneity of mucosal microbiota dynamics during colorectal cancer progression

Co-cultivation of microalgae-activated sludge for municipal wastewater treatment: Exploring the performance, microbial co-occurrence patterns, microbiota dynamics and function during the startup stage

Microalgae consortium is a promising technology for achieving low-carbon and resource utilization goals in municipal wastewater treatment. However, little is known about how the consortium affects the treatment performance in the startup stage of co-cultivation. Herein, photobioreactors were constructed with different contents of microalgae and activated sludge (AS) (wt.microalgae: wt.AS ≥ 50 %). The results showed that the concentration of microalgae increased by more than 20 % with AS, and the effluents were close or lower than Chinese discharge standards within HRT 24 h (NH4+-N, TP, and COD ≤ 5.0, 0.5, and 50 mg L-1). Furthermore, the co-occurrence pattern of microbial populations experienced inhibition-reconstruction and reconstruction-inhibition processes, respectively, and the inter-species relationship was directly related to the effluent quality. Microalgal concentration and temperature were the key factors to the microbial community profiling. The potential microorganisms in AS could promote the growth of microalgae, and the bacteria and fungi formed co-metabolism through functional complementation.

Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process

The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02–0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.

Fluorescence-Activating and Absorption-Shifting Nanoprobes for Anaerobic Tracking of Gut Microbiota Derived Vesicles.

Outer membrane vesicles (OMVs) are crucial for bacterial intercellular communication and the crosstalk between the gut microbiota and its host. Methods capable of visualizing gut microbiota derived OMVs would be of great significance but have been rarely reported. Here, nanoprobes carrying a fluorescence-activating and absorption-shifting tag are prepared by combining genetic engineering and antibiotic-boosted vesicle formation and release. Benefiting from their natural structure and molecular oxygen-independent emission, the resulting nanovesicles can be applied as endogenous fluorescence probes to anaerobically track gut microbiota associated OMVs. These nanoprobes show flexibility in on-demand fluorescence turn-on/off and reversibly switchable emission bands for intelligent and dual-color imaging. With these special characteristics, the behaviors of microbiota OMVs to not only inhibit specific pathogenic strains through membrane fusion but also repair the intestinal barrier via entering intestinal epithelia and promoting the expressions of tight junctions are tracked and identified in the gut. Based on these discoveries, OMVs are disclosed to be able to remit inflammation in a murine model of colitis following transplantation to the intestine by oral delivery. This work provides an approach to visualize the dynamics of the gut microbiota and disclose potential targets for disease intervention.