High-throughput 16S rRNA Gene Research Articles

Mildly acidic pH boosts up CO2 conversion to isobutyrate in H2 driven gas fermentation system.

As a greenhouse gas, massive carbon dioxide (CO2) has been generated due to organic matter degradation in wastewater treatment processes. Microbial gas fermentation offers a promising approach to capture CO2 and generate various valuable chemicals. However, limited studies have achieved branched or medium-chain fatty acids production via gas fermentation. This study reported the production of isobutyrate and hexanoate by feeding H2 and CO2 into membrane biofilm reactors (MBfRs). The gas fermentation product in the reactor with neutral pH (pH of 7) was dominated by acetate (accounting for 90 % of the product spectrum), whereas a mildly acidic pH (pH of 6) resulted in isobutyrate and hexanoate as the dominant products, with a selectivity of 57 % and 42 %, respectively. Notably, a remarkably high concentration of isobutyrate (266 mmol C/L) was produced in the reactor with pH of 6. Subsequent batch test results suggest that the isobutyrate production in this study is coupled with acetogenesis and ethanol-driven chain elongation processes, rather than via methanol-driven chain elongation reported previously. High-throughput 16S rRNA gene amplicon sequencing revealed that the microbial community under neutral pH was dominated by acetate-producing homoacetogens Acetobacterium. By contrast, a mildly acidic pH promoted the community shifting towards chain elongation microorganisms, dominated by Clostridium sensu stricto 12, Oscillibacter and Caproiciproducens. Collectively, this study demonstrates the significant role of mildly acidic pH in boosting up bioisomerization and chain elongation in gas fermentation systems, thus triggering isobutyrate and hexanoate production. The findings highlight gas fermentation as a new green alternative route for generating highly valuable isobutyrate and hexanoate.

Dynamic Impact of One-Year Integrated Rice-Crayfish Farming on Bacterioplankton Communities in Paddy Water.

As global food security issues become increasingly severe, an important innovation in agricultural production patterns, namely integrated rice-fish farming, has been widely implemented around the world, especially in Asia. To assess the impact of integrated rice-crayfish (Procambarus clarkii) farming (IRCF) on agricultural ecosystems, we used Illumina high-throughput 16S rRNA gene sequencing to analyze differences in diversity, composition, co-occurrence network, and assembly process of planktonic bacterial communities in paddy water between traditional rice farming (TRM) and IRCF. Environmental factors and planktonic bacterial communities were evaluated during the tillering, jointing, flowering, and grain-filling stages on August 24, September 5, September 24, and October 16, respectively. Our findings revealed that, throughout the entire cultivation period, IRCF had no notable impacts on bacterioplankton community diversity in paddy water, but it changed the composition and relative abundance of the dominant bacterioplankton. Specifically, IRCF promoted the Chloroflexota during the tillering stage but reduced its presence during the grain-filling stage. It also significantly decreased the Bacillota during the jointing stage while notably enhancing Actinomycetota during the flowering stage. Furthermore, IRCF markedly improved the robustness and negative/positive cohesion within bacterioplankton co-occurrence networks during jointing and grain-filling stages. IRCF altered the assembly processes shaping planktonic bacterial communities, promoting a greater dominance of stochastic processes during the tillering, jointing, and flowering stages and a diminished dominance during the grain-filling stage. IRCF dramatically changed aquatic environmental factors, particularly during the jointing stage, by substantially increasing the TN, ammonium, nitrate, and phosphate levels in paddy water. These nutrient levels were closely correlated with the dynamics of the planktonic bacterial communities. Our findings underscore the considerable potential of IRCF in enhancing the stability of bacterioplankton communities and promoting rice growth while also providing valuable data and theoretical insights into the microbiological ecological impacts of IRCF on the agroecosystem.

Exploring the Adaptation Process of Huso dauricus to High Temperatures Based on Changes in Intestinal Microbiota.

Global warming has led to rising water temperatures, posing a significant threat to fish survival. Understanding the mechanisms by which fish respond to and adapt to temperature variations is thus of considerable importance. This study employed high-throughput 16S rRNA gene sequencing and bioinformatics to investigate changes in the intestinal microbiota of the kaluga sturgeon (Huso dauricus) under four temperature conditions (19 °C, 25 °C, 28 °C, and 31 °C) and its relationship with adaptation to high-temperature stress. The results indicated that temperature variations caused significant changes in the intestinal microbiota. Over time, differences in the microbiota structure became more pronounced under different temperature conditions, and within-group variability gradually decreased. At higher temperatures, the relative abundance of Sphingomonas significantly decreased, while that of Clostridium sensu stricto 1, Cetobacterium, and Plesiomonas exhibited a significant increase in relative abundance. Upon the cessation of rapid mortality under various high-temperature conditions, the intestinal microbiota structure and composition became highly similar, with Clostridium sensu stricto 1 dominating both in terms of composition and relative abundance, suggesting a central role in adaptation to high-temperature stress. This study preliminarily confirms that the high-temperature adaptability of Huso dauricus is closely related to the structure and composition of its intestinal microbiota, with bacteria such as Clostridium sensu stricto 1 playing an important role. These findings provide new scientific insights into enhancing fish adaptability to high-temperature stress.

Microbial diversity and environmental determinants at Shanghai Hongqiao railway station: A comprehensive microbial assessment.

The COVID-19 pandemic has underscored the importance of indoor environmental management in transportation hubs, which are critical for pathogen transmission due to high foot traffic. However, research has primarily focused on subways, with limited studies on train stations. In this study, samples were collected at the Shanghai Hongqiao Railway Station in winter, spring, and summer. Microbial DNA was extracted from collected indoor surfaces and ambient air samples and then analyzed through high-throughput 16S rRNA gene sequencing. Alongside sample collection, environmental data were recorded. Alpha diversity was greatest in winter, followed by summer, and least in spring within the train station environment. Surface samples exhibited higher alpha diversity compared to air samples, with no notable difference between indoor and outdoor air. Beta diversity showed significant variation across seasons and locations, with seasonal changes more pronounced than spatial ones, primarily due to differences between air and surface samples rather than indoor and outdoor environments. Key determinants of microbial community structure included CO2, temperature, illuminance, and passenger volume. The microbial community in train stations originates from various sources, with contributions from both natural elements (like wastewater/sludge, soil, and plants) and human sources (such as gastrointestinal, oral, and dermal flora). This study highlights the microbial ecology of train stations, emphasizing the need for microbial surveillance and management in transportation settings.

Continuous Cropping of Patchouli Alleviate Soil Properties, Enzyme Activities, and Bacterial Community Structures.

Pogostemon cablin (Patchouli), an essential medicinal plant in the Lamiaceae family, faces significant challenges under continuous cropping (CC) obstacles. This study examined the rhizospheric soil bacterial communities of patchouli under four different CC years, zero (CK), one (T1), two (T2), and three (T3) years through high-throughput 16S rRNA gene amplicon sequencing. Results showed long-term CC led to significant soil properties and enzyme activity shifts. Key parameters such as soil pH and total potassium (TK) decreased, while ammonium nitrogen (NH4+-N), soil organic carbon (SOC), nitrate nitrogen (NO3--N), available potassium (AK), available phosphorus (AP), total nitrogen (TN), and total phosphorus (TP) increased over the cropping years. Enzyme activities, including ß-glucosidase (ß-GC), polyphenol oxidase (PPO), catalase (CAT), N-acetyl-β-D-glucosaminidase (NAG), and leucine aminopeptidase (LAP), were notably affected. The CC altered the bacterial community structure and composition, reducing the relative abundance of Proteobacteria, Firmicutes, Actinobacteria, and Planctomycetota over time. These findings highlight the impact of CC on patchouli rhizosphere bacteria, providing insights for improved soil management and fertilization strategies in CC systems.

Evaluation of the cervical liquid-based cytology sample as a microbiome resource for dual diagnosis.

Cervical cancer, which is mainly caused by oncogenic human papillomavirus subtypes, remains a significant global health challenge. Recent studies have indicated a connection between cervical cancer and the uterine microbiome, underscoring its importance. This study explored the potential of liquid-based cytology (LBC) samples, which are typically used for cytological analysis, in investigating the cervical microbiome. Thirty women participated in the study and provided clinical information. Three samples were obtained from each participant: one for clinical purposes using LBC, another for microbiome sampling using LBC, and a third using the SWAB Microbiome kit. The LBC and traditional swab (SWAB) samples were subjected to high-throughput 16S rRNA gene sequencing for microbiome analysis. The results revealed a consistent dominance of key taxa, particularly Lactobacillus spp. The analysis of differential abundance highlighted variations in microbial abundance among individuals, which were more prominent than those resulting from the sampling methods. Functional analysis identified arachidonic acid and alpha-linolenic acid metabolism, along with a cautionary note regarding the low mean proportion values. The network analysis revealed positive correlations between indicators of structure among the networks, highlighting the robustness of microbiome similarities despite the diversity of sampling methods. Supervised machine learning has revealed challenges in distinguishing LBC and SWAB samples based on their microbiome features. Weighted co-expression network analysis revealed that the correlation between microbial clusters and the sampling method with clinical data was not significant. This study emphasizes the similarity in microbial communities observed using the LBC and SWAB methods, highlighting the potential of using dual diagnostic approaches. Additionally, the use of residual LBC samples in large-scale microbiological studies can provide comprehensive insights into cervical health and disease.

Evaluating the Impact of Environmental Factors on Bacterial Populations in Riverine, Estuarine, and Coastal Sediments

Aquatic ecosystems, including rivers, estuaries, and coastal environments, are crucial for maintaining biodiversity, regulating nutrient cycles, and supporting human livelihoods. However, these ecosystems are increasingly being threatened by urbanization, making it essential to understand their microbial communities and their ecological roles. This study employed high-throughput 16S rRNA gene sequencing to characterize the bacterial communities within the riverine, estuarine, and coastal sediments of Adyar Creek, Chennai, India. Proteobacteria were the dominant phylum across most samples, with proportions ranging from 39.65% to 72.09%. Notably, the estuarine environment exhibited a distinct taxonomic profile characterized by a significant abundance of Firmicutes (47.09% of the bacterial population). Distinct bacterial classes were observed across sediment types: Alphaproteobacteria (30.07–34.32%) in riverine sediments, Bacilli dominated estuarine sediments (40.17%), and Gammaproteobacteria (15.71–51.94%) in coastal sediments. The most significant environmental factors influencing the bacterial community composition across these samples were pH, salinity, phosphate, and nitrate. LEfSe (Linear discriminant analysis Effect Size) analysis identified specific genera within the estuary, including Bacillus (20.26%), unclassified_Paenibacillus (12.87%), Clostridium (3.81%), Gailella (3.17%), Paenibacillus (3.02%), Massilia (1.70%), Paraburkholderia (1.42%), and Pantoea (1.15%), as potential biomarkers for habitat health. Functional analysis revealed an elevated expression of the genes associated with ABC transporters and carbon metabolism in the estuary, suggesting a heightened nutrient cycling capacity. Furthermore, co-occurrence network analysis indicated that bacterial communities exhibit a strong modular structure with complex species interactions across the three sediment types. These findings highlight bacterial communities’ critical role and the key drivers in estuarine ecosystems, establishing a baseline for further investigations into the functional ecology of these vulnerable ecosystems.

The functional dominance and metabolic diversity of comammox Nitrospira in recirculating aquaculture systems.

As a newly discovered group of ammonia-oxidizing microorganisms, complete ammonia oxidizing (comammox) Nitrospira has been widely found in various oligotrophic ecosystems. However, their activity and ecological niche is still unclear in recirculating aquaculture systems (RAS). This study aimed to compare the abundance and activity of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and elucidate metabolic versatility of comammox Nitrospira in RAS. Quantitative PCR (qPCR) results showed that either comammox Nitrospira or AOB numerically predominated, while comammox Nitrospira and AOA shared similar low ammonia niches. Specifically, DNA-based stable isotope probing in conjunction with high-throughput 16S rRNA gene amplicon sequencing revealed that comammox Nitrospira accounted for 79.1 %, 97.5 %, 91.9 % and 97.6 % in the active ammonia-oxidizing community in four selected typical samples representing high abundance of comammox, AOA, and AOB, respectively. Phylogenetic analysis of heavy fraction DNA further identified novel comammox species from Nitrospira nitrificans cluster and clade A.2 acting as active species in different freshwater aquariums. Moreover, metagenome-assembled genome analysis revealed them as novel species with stress resistance and metabolic diversity compared with known comammox Nitrospira. This study underscores the dominant role of comammox Nitrospira as active ammonia-oxidizers in RAS and presents two novel comammox MAGs with metabolic flexibility, enriching our understanding of the nitrification process in oligotrophic artificial ecosystems.

Seasonal Changes in the Gut Microbiota of Halyomorpha halys

The gut microbiome plays an important role in insect evolution and ecology. Bacteria support the host’s nutrition and defense and therefore play an important role in the fitness of the host. Halyomorpha halys is one of the most important invasive pest species in the world. Native to North-Eastern Asia, this Pentatomid bug has recently invaded North America and Europe, causing significant damage to agricultural production. Although an increasing number of studies investigated the biology of this pest species, little is known about the composition of its gut microbiota. Like many other Pentatomid species, H. halys harbors a primary symbiont called “Candidatus Pantoea carbekii,” which produces vitamins and essential amino acids for the host. However, information about the presence of other bacteria is currently lacking. Therefore, we investigated the gut microbiota of H. halys individuals, which were collected in the field across the year using a high-throughput 16S rRNA gene metabarcoding approach. Our results revealed 3309 different ASVs associated with H. halys, with Pantoea being the most abundant symbiont, present in almost all individuals. Additionally, many individuals harbor Commensalibacter, a genus of acetic acid bacterial symbionts. Besides these two predominant taxa, we show a high diversity of microorganisms associated with H. halys with seasonal fluctuations, highlighting a dynamic microbiota that might influence the biology of this species.

Composition of the Common Noctule (Nyctalus noctula) Gut Microbiota Determined by Bacteriological Analysis and High-Throughput 16S rRNA Gene Sequencing

Composition of the Common Noctule (Nyctalus noctula) Gut Microbiota Determined by Bacteriological Analysis and High-Throughput 16S rRNA Gene Sequencing

Bioremediation Potential of Rhodococcus qingshengii PM1 in Sodium Selenite-Contaminated Soil and Its Impact on Microbial Community Assembly.

Soil microbial communities are particularly sensitive to selenium contamination, which has seriously affected the stability of soil ecological environment and function. In this study, we applied high-throughput 16S rRNA gene sequencing to examine the effects of low and high doses of sodium selenite and the selenite-degrading bacterium, Rhodococcus qingshengii PM1, on soil bacterial community composition, diversity, and assembly processes under controlled laboratory conditions. Our results indicated that sodium selenite and strain PM1 were key predictors of bacterial community structure in selenium-contaminated soils. Exposure to sodium selenite initially led to reductions in microbial diversity and a shift in dominant bacterial groups, particularly an increase in Actinobacteria and a decrease in Acidobacteria. Sodium selenite significantly reduced microbial diversity and simplified co-occurrence networks, whereas inoculation with strain PM1 partially reversed these effects by enhancing community complexity. Ecological modeling, including the normalized stochasticity ratio (NST) and Sloan's neutral community model (NCM), suggested that stochastic processes predominated in the assembly of bacterial communities under selenium stress. Null model analysis further revealed that heterogeneous selection and drift were primary drivers of community turnover, with PM1 inoculation promoting species dispersal and buffering against the negative impacts of selenium. These findings shed light on microbial community assembly mechanisms under selenium contamination and highlight the potential of strain PM1 for the bioremediation of selenium-affected soils.

Drip irrigation affects soil bacteria primarily through available nitrogen and soil fungi mainly via available nutrients.

The issue of water scarcity is a global concern. Water-saving irrigation has long been a topic of interest among agricultural researchers. In this study, changes in soil microbial community structure and diversity under different periods of drip irrigation were analyzed using the Illumina HiSeq high-throughput sequencing platform and 16S rRNA gene sequence amplification. Six treatments were established based on varying drip irrigation amounts: maintaining the drip irrigation amount at 320 mm without any increase (CK), increasing by 72 mm during different growth stages: from the sowing stage to the jointing stage (J), from the jointing stage to the big trumpet stage (B), from the big trumpet stage to the tasseling stage (T), from the tasseling stage to the grain filling stage (G), and from the grain filling stage to the maturity stage (M). Compared to CK, the T treatment significantly increased the Chao index of soil bacteria by 2.95%. The main bacterial phyla included Proteobacteria, Acidobacteria, blastomonas, Actinobacteria, Chloromycetes, and Bacteroidetes, while ascomycetes, basidiomycetes, chytridomycetes, and mortieromycetes were the main fungal phyla across different periods of drip irrigation. Zoopagales, Amtridomyces, and Trichomyces were absent in the G, T, and M treatments, respectively. The content of soil-available potassium in the T treatment was higher than that in other treatments, whereas the content of soil-available nutrients in the B treatment was the lowest. Overall, the T treatment had the highest content of available nutrients. Redundancy analysis showed that available nitrogen was the main soil chemical property affecting soil bacterial community structure, while soil-available nutrients were the main soil chemical property affecting the fungal community structure. Thus, the T treatment was effective in enhancing soil microbial community structure and increasing soil-available nutrients.

Application of an anaerobic reactor for the treatment of sulfide-rich wastewater using biogas for H2S removal.

Anaerobic treatment of sulfur-rich wastewater is challenging because sulfide greatly inhibits the activity of anaerobic microorganisms, especially methanogenic archaea. We developed an internal phase-separated reactor (IPSR) that removed sulfide prior to methanogenesis by gas stripping using biogas produced in the reactor. The IPSR was fed with synthetic wastewater containing a very high sulfide concentration of up to 6,000 mg S L-1 with a chemical oxygen demand (COD) of 30,000 mg L-1. The IPSR was operated at an organic loading rate of 5-12 kg COD m-3 day-1 at 35 °C. The results show that the sulfide concentration was reduced from 6,000 mg S L-1 in the influent to <700 mg S L-1 in the first-stage effluent. The second-stage effluent contained <400 mg S L-1. As a result of effective sulfide removal by its gas stripping function, the IPSR had a COD removal efficiency of >90% over the entire experimental period. High-throughput 16S rRNA gene sequencing revealed that the major anaerobic archaea were Methanobacterium and Methanosaeta, which are frequently found in high-rate anaerobic reactors. Thus, the IPSR maintains these microorganisms and achieves high-process performance even when fed wastewater with very high sulfide concentrations.

Immunoglobulin-coating patterns reveal altered humoral responses to gut bacteria in pediatric cow milk allergies

BackgroundPediatric cow milk allergies (CMA) can occur in immunoglobulin (Ig) E and non-IgE-mediated forms. Unlike IgE-mediated allergies, the mechanisms of disease pathogenesis in non-IgE-mediated food allergy and an association with microbiome has not been well established. Previous studies have identified the presence of altered humoral responses to gut bacteria in IgE mediated allergies. Here, we analyzed IgA, IgE and IgG responses to gut bacteria in subjects with either IgE or non-IgE mediated CMA to identify relative proportions of Ig-coated bacteria and characterize unique disease specific microbial signatures.MethodsMulti-parametric flow cytometry analysis was used to identify IgA, IgE and IgG responses to gut bacteria in CMA patients. Cell sorting of Ig coated gut bacteria was subsequently performed followed by high throughput 16S rRNA gene sequencing and specific patterns of humoral responses to gut bacteria assessed in each study group.ResultsWe identified significant alterations in IgA and IgG gut bacterial coating patterns in CMA subjects. Proportions of IgA-coated bacteria were decreased in IgE mediated CMA subjects without atopic dermatitis (ALL) and non-IgE mediated CMA subjects (ENP), compared to healthy controls (CON). In comparison, IgG-coated bacteria was significantly elevated in CMA subjects with atopic dermatitis (AD). Alpha and beta diversities displayed significant differences in IgA-, IgE-, and IgG-coated bacteria in AD and ENP groups. Significant differences in bacteria coated by IgA, IgE and IgG were detected at Phyla, Genus and Species levels and associated bacterial dysbiosis in IgE and non-IgE mediated allergies were identified. Linear discriminant analysis (LDA) effect size (LEFse) revealed unique disease associated bacterial signatures, including several pathogenic bacteria namely Bacteroides fragilis, Ruminococcus gnavus, Eubacterium dolichum, Fusobacterium, Clostridium neonatale and Robinsoniella peoriensis. Receiver operating characteristic curve analysis confirmed the efficiency of using the bacterial signatures identified as biomarkers for disease.ConclusionsAltered IgA and IgG responses to gut bacteria were identified in CMA subjects. The disease-specific responses were associated with alterations in bacterial diversity and concomitant dysbiosis of Ig-coated bacteria in IgE-mediated and non-IgE-mediated CMA pediatric subjects. The identification of pathogenic bacteria uniquely associated with different classes of allergic disease indicates a role of these bacteria in driving disease-specific pathological phenotypes.

Improved treatment of coking wastewater and higher biodiversity through immobilization of Comamonas sp. ZF-3 supplemented microbial community.

The aim of this study was to investigate the relationship among pollutant removal performance, microbial community structure, and potential gene function of immobilized microorganisms in coking wastewater (CWW) treatment process. The results showed that the immobilized biomass containing strain Comamonas sp. ZF-3 displayed greater resistance to CWW and higher COD, NH4+-N removal efficiency (92%, 60%) than free cells (48%, 7%), meanwhile, the results from GC-MS proved main organic pollutants in CWW including phenolic compounds, heterocyclic compounds, and polycyclic aromatic hydrocarbons were basically removed by immobilized microorganisms. During 123 days of degradation experiment, high-throughput 16S rRNA gene sequencing analysis of immobilized carriers showed more stable and diverse microbial community, which was consistent with simultaneous removal of COD and NH4+-N observed in carrier experiment. Among them, Comamonas sp. ZF-3 continuously remained at the highest proportion (23.25%) in immobilized carrier, while Nitrosomonas (1.47%) and Nitrospira (1.90%) were simultaneously detected. Moreover, microbial community of immobilized carriers showed higher relative abundance of potential function in membrane transport and xenobiotics biodegradation and metabolism, which may indirectly displayed biodegradation activity of immobilized functional microorganisms. This work illustrated the survival status and potential gene function of immobilized microorganisms, and provided basis for practical application of immobilized carriers in CWW treatment.

Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home.

Frailty increases the risk of needing nursing care and significantly affects the life and functional prognosis of older individuals. Early detection and tailored interventions are crucial for maintaining and enhancing their life functions. Recognizing distinct clinical phenotypes is essential for devising appropriate interventions. This study aimed to explore diverse frailty phenotypes, focusing on poor nutrition in older Japanese individuals through observational research. Twenty-one nursing home residents underwent a comprehensive survey covering physical, blood, dietary, cardiac, cognitive, nutritional, nursing care, frailty, agitated behavior, and gut microbiome assessments (high-throughput 16S rRNA gene sequencing). Using clustering analysis with 239 survey items (excluding gut microbiome), participants were classified into subgroups based on clinical phenotypes, and group characteristics were compared through analysis. Individuals with moderate or severe frailty and suspected dementia formed subgroups with distinct clinical phenotypes based on nutritional, defecation, and nursing care statuses. The gut microbiome significantly varied among these groups (p = 0.007), indicating its correlation with changes in clinical phenotype. Nutritional status differences suggested poor nutrition as a differentiating factor in the core clinical phenotype. This study proposes that the gut microbiome differs based on the clinical phenotype of Japanese older individuals with frailty, and targeted interventions addressing the gut microbiome may contribute to preventing frailty in this population.

Fimbriimonadales performed dissimilatory nitrate reduction to ammonium (DNRA) in an anammox reactor

Bacteria belonging to the order Fimbriimonadales are frequently detected in anammox reactors. However, the principal functions of these bacteria and their potential contribution to nitrogen removal remain unclear. In this study, we aimed to systematically validate the roles of Fimbriimonadales in an anammox reactor fed with synthetic wastewater. High-throughput 16S rRNA gene sequencing analysis revealed that heterotrophic denitrifying bacteria (HDB) were the most abundant bacterial group at the initial stage of reactor operation and the abundance of Fimbriimonadales members gradually increased to reach 38.8 % (day 196). At the end of reactor operation, Fimbriimonadales decreased to 0.9 % with an increase in anammox bacteria. Correlation analysis demonstrated nitrate competition between Fimbriimonadales and HDB during reactor operation. Based on the phylogenetic analysis, the Fimbriimonadales sequences acquired from the reactor were clustered into three distinct groups, which included the sequences obtained from other anammox reactors. Metagenome-assembled genome analysis of Fimbriimonadales allowed the identification of the genes narGHI and nrfAH, responsible for dissimilatory nitrate reduction to ammonium (DNRA), and nrt and nasA, responsible for nitrate and nitrite transport. In a simulation based on mass balance equations and quantified bacterial groups, the total nitrogen concentrations in the effluent were best predicted when Fimbriimonadales was assumed to perform DNRA (R2 = 0.70 and RMSE = 18.9). Moreover, mass balance analysis demonstrated the potential contribution of DNRA in enriching anammox bacteria and promoting nitrogen removal. These results prove that Fimbriimonadales compete with HDB for nitrate utilization through DNRA in the anammox reactor under non-exogenous carbon supply conditions. Overall, our findings suggest that the DNRA pathway in Fimbriimonadales could enhance anammox enrichment and nitrogen removal by providing substrates (nitrite and/or ammonium) for anammox bacteria.

Changes in the intestinal microbiome of the preterm baby associated with stopping non-invasive pressure support: a prospective cohort study

BackgroundIntestinal dysbiosis is implicated in the pathogenesis of necrotising enterocolitis and late-onset sepsis in preterm babies. The provision of non-invasive positive pressure ventilation is a common clinical intervention in preterm...

Linking Microbiota Profiles to Disease Characterization in Common Variable Immunodeficiency: The Case of Granulomatous-Lymphocytic Interstitial Lung Disease.

Background and objectives: Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by decreased immunoglobulins and recurrent infections, with non-infectious complications such as granulomatous-lymphocytic interstitial lung disease (GLILD) affecting up to 30% of patients. Methods: Using high-throughput 16S rRNA gene sequencing, salivary, sputum, and fecal microbiome from CVID patients with GLILD, comparing them to CVID patients without GLILD-with immune dysregulation (dCVID) and only infections (iCVID)-and healthy controls was analyzed. Results: A total of 41 CVID patients, 7 with GLILD, and 15 healthy donors were included. Global fecal biodiversity was significantly lower in GLILD patients compared to CVID subgroups and controls. GLILD patients harbored different specific bacterial communities in all niches, with some keystone species common to dCVID. Conchiformibius, Micrococcales, and Capnocytophaga are more frequent in the sputum of GLILD patients. Saliva in GLILD shows higher frequencies of Conchiformibius and Haemophilusparainfluenzae. Fecal samples from GLILD patients have higher levels of Gemella morbilorum, Lacticaseibacillus, and Cellulosimicrobium. A non-assigned Conchiformibius spp. is consistently associated with GLILD across different niches and could be a potential pathobiont or relevant microbiological marker for GLILD. Cluster network and correlation analyses show profound dysbiosis in the sputum, saliva, and feces of GLILD patients. Conclusions: These findings highlight significant microbiome alterations in CVID patients with GLILD, particularly in the respiratory tract, suggesting a possible link to both local and systemic immune dysregulation.

Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).

Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.