V3 Sequences Research Articles

Discovery of <i>Brevibacterium</i> predominating in fecal samples from three children with persistent diarrhea negative for common pathogens

Acute diarrhea is a common disease in children under 5 years old and can develop into persistent diarrhea, greatly affecting the children's health. Although advanced techniques had been used to diagnose and detect common pathogens in hospitals, however, 40% of cases are negative for the pathogens. In this study, to investigate dominant bacteria in stool samples of three persistent-diarrheal children with unidentified pathogenic agents, the V3 and V68 regions of the 16S rRNA gene were amplified from fecal bacterial metagenomic DNA, separated on DGGE gel, and the dominant DNA bands were sequenced. As a result, the V3 and V68 regions of bacteria in persistent diarrheal children were less diverse and different from the corresponding DNA bands of the indicator strains. Sequence analysis and similarity comparison of six DNA bands of V3 regions and seven DNA bands of V68 regions showed that two V3 sequences (of 160 bp) derived from two samples were novel and did not match any genes from the non-redundant database, but they shared 93.75% similarity to each other. The four V3 sequences left derived from all three samples were the most similar (94.53-100%) with the corresponding genes of Brevibacterium. Six of the seven V68 sequences derived from dominant DNA bands of all three samples were the most similar (from 99.4% to 100%) to the corresponding genes of referent strains belonging to the genus Enterococcus. In sample D3, a sequence of the V68 region possessed 100% identity to the E. faecalis ATCC 19433 strain. This is the first study report that Brevibacterium was the dominant bacteria in the gastrointestinal microflora of children with persistent diarrhea although the bacterial genus has been reported to cause dangerous diseases in humans with immunodeficiency.

Paired comparison of the analytical performance between the Oncomine™ Comprehensive Assay v3 and whole-exome sequencing of ovarian cancer tissue

BackgroundNext-generation sequencing (NGS) has been implemented in clinical oncology as a personalized medicine tool to identify targetable genetic alterations and to guide treatment decisions. However, the optimal NGS test strategy and target genes for clinical use are still being discussed. The aim was to compare the performance of the Oncomine™ Comprehensive Assay v3 (OCAv3) (targeted gene panel) and whole-exome sequencing (WES) to investigate somatic single and multiple nucleotide variants and small indels in ovarian cancer patients.Methods and resultsGenomic DNA was isolated from fresh frozen samples of five high-grade serous (HGSC) and three clear cell ovarian (oCCC) cancer patients. Exome sequencing libraries were prepared by using the Ion AmpliSeq Exome RDY kit, whereas libraries for OCAv3 were prepared using by Ion AmpliSeq™ Library Kit Plus. Sequencing was performed using the Ion S5XL System (Thermo Fisher Scientific). When including only variants classified as pathogenic, likely pathogenic or unknown significance based on ClinVar database verdicts and comparing overlapping regions covered both by the OCAv3 assay and WES, 23 variants were detected by both assays. However, OCAv3 detected additionally two variants: ARID1A: p.Gln563Ter and TP53: p.Ser261ValfsTer84 that have not passed WES filtering criteria due to low coverage.ConclusionsWith the present treatment possibilities, OCAv3 panel testing provided higher diagnostic yield due to better coverage. Our study emphasizes that WES, although offering the potential to identify novel findings in genes not covered by OCAv3, might overlook variants in genes relevant for OC.

Combining Organic and Inorganic Fertilization Enhances Soil Enzyme Activity, the Bacterial Community, and Molecular Ecological Network Complexity in Coal Mine Reclamation Areas

Combined organic and inorganic fertilization can improve soil fertility in coal mine reclamation areas. However, the contribution of the bacterial community (especially its occurrence patterns) to soil physicochemical properties and enzyme activity needs further evaluation. The objective of this research was to clarify the bacterial community diversity, composition, and intraspecific interactions in response to combined organic and inorganic fertilizer application in coal mine reclamation areas in the Loess Hilly Region, China. Maize rhizosphere soil samples were collected under four fertilization regimes (CK, no fertilization control; NPK, compound inorganic fertilizer; M, organic fertilizer; and NPKM, combined organic and inorganic fertilization) in a 10-year field experiment in Gujiao city, Shanxi Province. Bacterial communities were characterized using high-throughput sequencing of the 16S rRNA gene V3–V4 region. A cross-treatment Spearman correlation network was constructed to explore the bacterial co-occurrence patterns. Compared with CK, NPK, M, and NPKM decreased the pH by 0.59%, 2.27%, and 0.12%; increased the soil organic carbon by 11.25%, 11.69%, and 27.05%; and significantly decreased the bacterial Shannon diversity by 3.68%, 0.14%, and 3.54%, respectively. Compared with CK, NPKM significantly increased sucrase, urease, and alkaline phosphatase activities (p < 0.05). Critically, oligotrophic Acidobacteria were significantly more abundant in CK than in the other treatments. Gemmatimonadetes were more abundant in NPK and M, and Actinobacteria, Bacteroidota, and Patescibacteria were more abundant in NPKM. In addition, network analysis revealed that the keystone taxa in the different fertilization treatments belonged to different network modules and were significantly correlated with soil nutrient content and enzyme activity. Simultaneously, the Actinobacteria enriched in NPKM formed specific clusters through strong symbiosis, and there were significant positive correlations among sucrase, urease, and alkaline phosphatase. In summary, long-term combined organic and inorganic fertilization improved maize rhizosphere soil fertility by regulating enzyme activity, bacterial community composition, and bacterial species interactions in coal mine reclamation areas in the Loess Hilly Region.

Dysbiosis and Staphylococcus species over representation in the exit site skin microbiota of hemodialysis patients carrying tunneled cuffed central venous catheter

Objectives Hemodialysis patients with end-stage renal disease (ESRD) are susceptible to infections and dysbiosis. Catheter-related infections are typically caused by opportunistic skin pathogens. This study aims to compare the skin microbiota changes around the exit site of tunneled cuffed catheters (peri-catheter group) and the contralateral site (control group). Methods ESRD patients on hemodialysis were recruited. The skin microbiota were collected with moist skin swabs and analyzed using high-throughput sequencing of the 16S rDNA V3–V4 region. After denoising, de-replication, and removal of chimeras, the reads were assigned to zero-radius operational taxonomic units (ZOTU). Results We found significantly reduced alpha diversity in the peri-catheter group compared to the control group, as indicated by the Shannon, Jost, and equitability indexes, but not by the Chao1 or richness indexes. Beta diversity analysis revealed significant deviation of the peri-catheter microbiota from its corresponding control group. There was an overrepresentation of Firmicutes and an underrepresentation of Actinobacteria, Proteobacteria, and Acidobacteria at the phylum level in the peri-catheter group. The most abundant ZOTU (Staphylococcus spp.) drastically increased, while Cutibacterium, a commensal bacterium, decreased in the peri-catheter group. Network analysis revealed that the skin microbiota demonstrated covariance with both local and biochemical factors. Conclusions In conclusion, there was significant skin microbiota dysbiosis at the exit sites compared to the control sites in ESRD dialysis patients. Managing skin dysbiosis represents a promising target in the prevention of catheter-related bacterial infections.

Mafic veins in the mantle section of the Oman ophiolite: Petrological and geochronological insights from the Oman Drilling Project cores

The magmatic and tectonic evolution of the Oman ophiolite was investigated using the core samples obtained in the Oman Drilling Project. The core samples were recovered from three drilling sites (BA1B, BA3A, and BA4A) in the mantle section composed mainly of harzburgite and discordant dunite and wehrlite. A large number of mafic veins crosscut the structures of both mantle lithologies, indicating that they intruded after the formation of discordant dunites. The wehrlites include Fe3+-rich and TiO2-poor chromian spinel, suggesting that the discordant dunites and wehrlites were involved in hydrous, Ti-poor arc magmatism. The composition of plagioclase and clinopyroxene and rare-earth element (REE) patterns of clinopyroxene for the mafic veins suggest that the mafic veins were produced from mid-ocean ridge basalt (MORB)-like parental melts. On the other hand, early crystallization of clinopyroxene and Fe3+-rich and TiO2-poor chromian spinel in the mafic veins imply that the parental melts were also hydrous. Zircon UPb dating of the mafic veins yields the igneous age of about 91 Ma, which is younger than the V1 and V2 volcanic sequences. Depending on the distance from the mafic veins, the various REE patterns of clinopyroxene and Ca amphibole in the Oman harzburgites indicate local peridotite metasomatism during intrusion and percolation of late-stage melts that formed the mafic veins. Ca amphibole in the harzburgites and mafic veins lack significant enrichment in fluid-mobile elements, indicating that the hydrous phases were formed by fluids associated with hydrothermal activities in a spreading environment instead of slab-derived fluids. The mafic veins were likely produced in a spreading environment on a supra-subduction zone. As their formation took place after the arc magmatism that formed the Oman V2 lava sequence and discordant dunites, as a result of slab roll-back. This seafloor re-spreading on a supra-subduction zone after the V2 magmatism recorded in the mantle section might have been involved in the formation of the plume-related V3 lava sequence overlying the V2 lavas.

Effect of Mild Organic Substitution on Soil Quality and Microbial Community

Mild organic substitution is advantageous for sustainable agricultural development. In order to determine the proper fertilization strategy, it is essential to investigate the impact of substituting chemical fertilizers with varying levels of organic manure on soil nutrients, microbial communities, and crop productivity. Four treatments were implemented: no fertilizer, sole chemical fertilizer, 20% organic manure substitution, and 40% organic manure substitution. Bacterial and fungal communities were characterized through high-throughput sequencing of the 16S rRNA gene V3–V4 region and the V4 region, respectively. The 20% and 40% organic manure substitutions increased soil organic matter (SOM) content, total nitrogen (TN) content, and reduced soil pH compared to the control (CK). The 20% organic manure substitution showed the most significant improvements in soil alkaline phosphatase, urease, and invertase activities. Soil nutrient enhancement increased bacterial alpha diversity, with a milder impact on fungal alpha diversity compared to bacteria. Different fertilization treatments elevated the relative abundance of bacterial Bacteroidetes (8.11%, 21.25%, and 1.88%), Actinomycetes (12.65%, 26.36%, and 15.33%), and fungal Ascomycota (16.19%, 10.44%, and 12.69%), known for degrading recalcitrant organic matter. The sole chemical fertilizer treatment increased the pathogenic Cheatotryiales. Shared species, primarily from bacterial Actinomycetes, Firmicutes, Proteobacteria, and fungal Ascomycota phyla, were found at 20% and 40% organic manure substitution levels. Specifically, the 20% organic manure substitution level promoted the relative abundance of beneficial plant growth-promoting taxa, Oxalobacteraceae and Massilia, and suppressed pathogens, with an increase in the relative abundance of the Purpureocillium genus and Mortierellomycota. These findings suggest that a 20% OF substitution can maintain crop yield, enhance soil nutrients and enzyme activities by fostering beneficial soil bacteria, inhibiting soil-borne pathogens, and refining microbial community structure.

Oral microbiota signatures associated with viremia and CD4 recovery in treatment-naïve HIV-1-infected patients

PurposeFew reports focused on the role of oral microbiome diversity in HIV infection. We characterized the microbiota-immunity axis in a cohort of treatment-naïve HIV-1-infected patients undergoing antiretroviral therapy (ART) focusing on the oral microbiome (OM) and immunological responsivity. MethodsThe sequencing of 16S rRNA V3–V4 hypervariable region was performed on salivary samples of 15 healthy control (HC) and 12 HIV + patients before starting ART and after reaching virological suppression. Then, we correlated the OM composition with serum cytokines and the Short Chain Fatty acids (SCFAs). ResultsThe comparison between HIV patients and HC oral microbiota showed differences in the bacterial α-diversity and richness. We documented a negative correlation between oral Prevotella and intestinal valeric acid at before starting ART and a positive correlation between oral Veillonella and gut acetic acid after reaching virological suppression. Finally, an increase in the phylum Proteobacteria was observed comparing saliva samples of immunological responders (IRs) patients against immunological non-responders (INRs). ConclusionsFor the first time, we described an increase in the oral pro-inflammatory Proteobacteria phylum in INRs compared to IRs. We provided more evidence that saliva could be a non-invasive and less expensive approach for research involving the oral cavity microbiome in HIV patients.

Unveiling microbial degradation of triclosan: Degradation mechanism, pathways, and catalyzing clean energy

Emerging organic contaminants present in the environment can be biodegraded in anodic biofilms of microbial fuel cells (MFCs). However, there is a notable gap existing in deducing the degradation mechanism, intermediate products, and the microbial communities involved in degradation of broad-spectrum antibiotic such as triclosan (TCS). Herein, the possible degradation of TCS is explored using TCS acclimatized biofilms in MFCs. 95% of 5 mgL−1 TCS are been biodegraded within 84 h with a chemical oxygen demand (COD) reduction of 62% in an acclimatized-MFC (A-MFC). The degradation of TCS resulted in 8 intermediate products including 2,4 -dichlorophenol which gets further mineralized within the system. Concurrently, the 16S rRNA V3–V4 sequencing revealed that there is a large shift in microbial communities after TCS acclimatization and MFC operation. Moreover, 30 dominant bacterial species (relative intensity >1%) are identified in the biofilm in which Sulfuricurvum kujiense, Halomonas phosphatis, Proteiniphilum acetatigens, and Azoarcus indigens significantly contribute to dihydroxylation, ring cleavage and dechlorination of TCS. Additionally, the MFC was able to produce 818 ± 20 mV voltage output with a maximum power density of 766.44 mWm−2. The antibacterial activity tests revealed that the biotoxicity of TCS drastically reduced in the MFC effluent, signifying the non-toxic nature of the degraded products. Hence, this work provides a proof−of−concept strategy for sustainable mitigation of TCS in wastewaters with enhanced bioelectricity generation.

Public health risk assessment and speciation of air-borne microorganisms in an office building

This study focuses on speciation of air borne microbes in an office building and health impacts of these microbes in terms of Quantitative Microbial Risk Assessment (QMRA), Hazard Quotient (HQ) and Hazard Index (HI). This is important in the wake of Sustainability Development Goal 3 (Public Health and well-being) specially when there is a lack of standards in terms of microbial air quality in office buildings where people spend 8–10 h indoors. Air borne bacterial and fungal species in different floors of the office building with varying occupancy and work profile were identified. The load of bacterial count on an average for the entire building was found to be 1917 CFU/m3. Overall, Gram-positive bacteria were predominant (>53%). Based on V3–V4 sequencing Staphylococcus scuiri (causing UTIs) was the most abundant (93.7%) and other bacterial species found were Lactobacillus hamsteri, Prevotella copri, Bacteroides plebeius Faecalibacterium prausnitzii, Bacillus coagulans (gut commensals), Shigella boydii (causes bacillary dysentery), and Propionibacterium acnes (acne producing). Fungal load was 4000 CFU/m3. Based on ITS sequencing Aspergillus (45.6%) was the dominant fungus and other fungi found were Cunninghamella, Lichtheimia, Fusarium, and Circinella Grammothele, Chondrostereum, and Pseudolagarobasidium, Candida sp., Chondrostereum, Sarocladium. The QMRA of gram-negative air borne bacteria showed a high disease burden, well over the WHO benchmark values even though Hazard Quotient (HQ) and Hazard Index (HI) was found to be negligible. These findings can contribute to the development of guidelines for seemingly safe workplaces that may harbour disease-causing microbes and calls for an immediate attention from policy makers as it is a major cause of concern for public health.

Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy

BackgroundChildren with cancer receiving chemotherapy commonly report a cluster of psychoneurological symptoms (PNS), including pain, fatigue, anxiety, depression, and cognitive dysfunction. The role of the gut microbiome and its functional metabolites in PNS is rarely studied among children with cancer. This study investigated the associations between the gut microbiome–metabolome pathways and PNS in children with cancer across chemotherapy as compared to healthy children.MethodsA case–control study was conducted. Cancer cases were recruited from Children’s Healthcare of Atlanta and healthy controls were recruited via flyers. Participants reported PNS using the Pediatric Patient-Reported Outcomes Measurement Information System. Data for cases were collected pre-cycle two chemotherapy (T0) and post-chemotherapy (T1), whereas data for healthy controls were collected once. Gut microbiome and its metabolites were measured using fecal specimens. Gut microbiome profiling was performed using 16S rRNA V4 sequencing, and metabolome was performed using an untargeted liquid chromatography–mass spectrometry approach. A multi-omics network integration program analyzed microbiome–metabolome pathways of PNS.ResultsCases (n = 21) and controls (n = 14) had mean ages of 13.2 and 13.1 years. For cases at T0, PNS were significantly associated with microbial genera (e.g., Ruminococcus, Megasphaera, and Prevotella), which were linked with carnitine shuttle (p = 0.0003), fatty acid metabolism (p = 0.001) and activation (p = 0.001), and tryptophan metabolism (p = 0.008). Megasphaera, clustered with aspartate and asparagine metabolism (p = 0.034), carnitine shuttle (p = 0.002), and tryptophan (p = 0.019), was associated with PNS for cases at T1. Gut bacteria with potential probiotic functions, along with fatty acid metabolism, tryptophan, and carnitine shuttle, were more clustered in cancer cases than the control network and this linkage with PNS needs further studies.ConclusionsUsing multi-omics approaches, this study indicated specific microbiome–metabolome pathways linked with PNS in children with cancer across chemotherapy. Due to limitations such as antibiotic use in cancer cases, these findings need to be further confirmed in a larger cohort.

Unveiling the negative association of Faecalibacterium prausnitzii with ischemic stroke severity, impaired prognosis and pro-inflammatory markers

BackgroundThe correlation between acute ischemic stroke (AIS) and gut microbiota has opened a promising avenue for improving stroke prognosis through the utilization of specific gut bacterial species. This study aimed to identify gut bacterial species in AIS patients and their correlation with stroke severity, 3-month prognosis, and inflammatory markers. Methods: We enrolled 59 AIS patients (from June 2021 to July 2022) and 31 age-matched controls with similar cerebrovascular risk profiles but no stroke history. Fecal samples were analyzed using 16 S rDNA V3–V4 sequencing to assess α and β diversity and identify significant microbiota differences. AIS cases were categorized based on the National Institute of Health Stroke Scale (NIHSS) scores and 3-month modified Rankin Scale (mRS) scores. Subgroup analyses were performed, and correlation analysis was used to examine associations between flora abundance, inflammatory markers and stroke outcome. ResultsSignificant differences in β-diversity were observed between case and control groups (P < 0.01). Bacteroides dominated AIS samples, while Clostridia, Lachnospirales, Lachnospiraceae, Ruminococcaceae, Faecalibacterium, and Faecalibacterium prausnitzii were prominent in controls. Faecalibacterium and Faecalibacterium prausnitzii were significantly reduced in non-minor stroke and 3-month poor prognosis groups compared to controls, while this difference was less pronounced in patients with minor stroke and 3-month good prognosis. Both Faecalibacterium and Faecalibacterium prausnitzii were negatively correlated with the NIHSS score on admission (r = −0.48, −0.48, P < 0.01) and 3-month mRS score (r = −0.48, −0.44, P < 0.01). Additionally, they showed negative correlations with pro-inflammatory factors and positive correlations with anti-inflammatory factors (both P < 0.01). ConclusionsFaecalibacterium prausnitzii is negatively associated with stroke severity, impaired prognosis, and pro-inflammatory markers, highlighting its potential application in AIS treatments.

Microbiologic surveys for Baijiu fermentation are affected by experimental design

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

The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4

The application of high-throughput sequencing (HTS) technologies has revolutionized research on phytoplankton biodiversity by generating an unprecedented amount of molecular data in marine ecosystem surveys. However, high-level of molecular diversity uncovered in HTS-based metabarcoding analyses may lead to overinterpretation of phytoplankton diversity due to excessive intra-genomic variations (IGVs). The aims in this study are to explore the nature of phytoplankton molecular diversity and to test the hypothesis. We carried out single-cell metabarcoding analysis of 18S rDNA V4 sequences obtained in single Noctiluca scintillans cells isolated from various sites in coastal waters of China. Results showed that each single N. scintillans cell harbored a high level of IGVs with about 100 amplicon sequence variants (ASVs). The large numbers of non-dominant ASVs identified in N. scintillans cells, which might correspond to the larger numbers of ASVs annotated as N. scintillans and showed similar temporal dynamics in metabarcoding analyses, could inflate the inter-species diversity or intra-species genetic diversity. In addition, there were large numbers of additional ASVs that were not annotated as N. scintillans. These non-N. scintillans ASVs might represent diverse preys for N. scintillans, consistent with previous reports that N. scintillans may act as chance predator of a broad-spectrum preys. This single-cell study has unambiguously demonstrated that the existence of high levels of IGVs in N. scintillans and most likely many other phytoplankton species, demonstrating that the majority of the molecular diversity revealed in metabarcoding analysis, which were generally interpreted as the sum of inter-species diversity and intra-species diversity, actually included high levels of IGVs and should be interpreted with caution.

Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis

BackgroundThe studies on SARS-CoV-2 and human microbiota have yielded inconsistent results regarding microbiota α-diversity and key microbiota. To address these issues and explore the predictive ability of human microbiota for the prognosis of SARS-CoV-2 infection, we conducted a reanalysis of existing studies.MethodsWe reviewed the existing studies on SARS-CoV-2 and human microbiota in the Pubmed and Bioproject databases (from inception through October 29, 2021) and extracted the available raw 16S rRNA sequencing data of human microbiota. Firstly, we used meta-analysis and bioinformatics methods to reanalyze the raw data and evaluate the impact of SARS-CoV-2 on human microbial α-diversity. Secondly, machine learning (ML) was employed to assess the ability of microbiota to predict the prognosis of SARS-CoV-2 infection. Finally, we aimed to identify the key microbiota associated with SARS-CoV-2 infection.ResultsA total of 20 studies related to SARS-CoV-2 and human microbiota were included, involving gut (n = 9), respiratory (n = 11), oral (n = 3), and skin (n = 1) microbiota. Meta-analysis showed that in gut studies, when limiting factors were studies ruled out the effect of antibiotics, cross-sectional and case–control studies, Chinese studies, American studies, and Illumina MiSeq sequencing studies, SARS-CoV-2 infection was associated with down-regulation of microbiota α-diversity (P < 0.05). In respiratory studies, SARS-CoV-2 infection was associated with down-regulation of α-diversity when the limiting factor was V4 sequencing region (P < 0.05). Additionally, the α-diversity of skin microbiota was down-regulated at multiple time points following SARS-CoV-2 infection (P < 0.05). However, no significant difference in oral microbiota α-diversity was observed after SARS-CoV-2 infection. ML models based on baseline respiratory (oropharynx) microbiota profiles exhibited the ability to predict outcomes (survival and death, Random Forest, AUC = 0.847, Sensitivity = 0.833, Specificity = 0.750) after SARS-CoV-2 infection. The shared differential Prevotella and Streptococcus in the gut, respiratory tract, and oral cavity was associated with the severity and recovery of SARS-CoV-2 infection.ConclusionsSARS-CoV-2 infection was related to the down-regulation of α-diversity in the human gut and respiratory microbiota. The respiratory microbiota had the potential to predict the prognosis of individuals infected with SARS-CoV-2. Prevotella and Streptococcus might be key microbiota in SARS-CoV-2 infection.

Bacterial communities structure in constructed wetlands for municipal and industrial wastewater treatment in Tanzania

Abstract Bacteria are the largest and most essential microorganisms in wastewater treatment systems. Despite the vital role bacteria play in enhancing wastewater treatment, its community structure and diversity remain poorly known. This study elucidated bacterial diversity and community structure in constructed wetlands (CWs) for municipal and industrial wastewater treatment using a culture-independent approach. Analysis of physicochemical parameters and Illumina high-throughput sequencing of V3 and V4 hypervariable regions of 16S rRNA gene bacterial community was performed. The results showed that the Proteobacteria were dominant (48.66%) phyla across all CWs. The Gammaproteobacteria class (27.67%), family Comamonadaceae (35.79) and Genus Flavobacterium (4.35%) were dominant across studied CWs. Bacterial abundance increased from the inlet to the outlet, with CWs having a higher abundance around the outlet, showing a good performance. The Shannon–Wiener index showed the highest species diversity (H = 1.45) in Banana Investment Limited CWs treating industrial wastewater. This study found significant bacterial diversity across studied CWs, with higher abundance and diversity at the outlet indicating better performance than those with low abundance and diversity at the outlet. We recommend a longitudinal investigation at each CWs section to confirm and establish the role of bacterial diversity on the performance pattern of CWs.

Diversity of Bacteria Associated with Guts and Gonads in Three Spider Species and Potential Transmission Pathways of Microbes within the Same Spider Host.

Microbial symbiosis plays a crucial role in the ecological and evolutionary processes of animals. It is well known that spiders, with their unique and diverse predatory adaptations, assume an indispensable role in maintaining ecological balance and the food chain. However, our current understanding of spider microbiomes remains relatively limited. The gut microbiota and gonad microbiota of spiders can both potentially influence their physiology, ecology, and behavior, including aspects such as digestion, immunity, reproductive health, and reproductive behavior. In the current study, based on high-throughput sequencing of the 16S rRNA V3 and V4 regions, we detected the gut and gonad microbiota communities of three spider species captured from the same habitat, namely, Eriovixia cavaleriei, Larinioides cornutus, and Pardosa pseudoannulata. In these three species, we observed that, at the phylum level classification, the gut and gonad of E. cavaleriei are primarily composed of Proteobacteria, while those of L. cornutus and P. pseudoannulata are primarily composed of Firmicutes. At the genus level of classification, we identified 372 and 360 genera from the gut and gonad bacterial communities. It is noteworthy that the gut and gonad bacterial flora of E. cavaleriei and L. cornutus were dominated by Wolbachia and Spiroplasma. Results show that there were no differences in microbial communities between females and males of the same spider species. Furthermore, there is similarity between the gut and ovary microbial communities of female spiders, implying a potential avenue for microbial transmission between the gut and gonad within female spiders. By comprehensively studying these two microbial communities, we can establish the theoretical foundation for exploring the relationship between gut and gonad microbiota and their host, as well as the mechanisms through which microbes exert their effects.

Gut bacterial population and community dynamics following adult emergence in pest tephritid fruit flies

Gut microbiota are important contributors to insect success. Host-microbe interactions are dynamic and can change as hosts age and/or encounter different environments. A turning point in these relationships the transition from immature to adult life stages, particularly for holometabolous insects where there is radical restructuring of the gut. Improved knowledge of population and community dynamics of gut microbiomes upon adult emergence inform drivers of community assembly and physiological aspects of host-microbe interactions. Here, we evaluated the bacterial communities of the pest tephritid species melon fly (Zeugodacus cucurbitae) and Medditeranean fruit fly (medfly, Ceratitis capitata) associated with the pupae life stage and timepoints immediately following adult eclosion. We used a combination of culturing to determine cultivatable bacterial titers, qPCR to determine 16S-rRNA SSU copy numbers, and 16S V4 sequencing to determine changes in communities. Both culturing and qPCR revealed that fly bacterial populations declined upon adult emergence by 10 to 100-fold followed by recovery within 24 h following eclosion. Titers reached ~ 107 CFUs (~ 108 16S rRNA copies) within a week post-emergence. We also observed concurrent changes in amplicon sequence variance (ASVs), where the ASV composition differed overtime for both melon fly and medfly adults at different timepoints. Medfly, in particular, had different microbiome compositions at each timepoint, indicating greater levels of variation before stabilization. These results demonstrate that tephritid microbiomes experience a period of flux following adult emergence, where both biomass and the makeup of the community undergoes dramatic shifts. The host-microbe dynamics we document suggest plasticity in the community and that there may be specific periods where the tephritid gut microbiome may be pliable to introduce and establish new microbial strains in the host.

Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field.

Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well. Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis. From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas, and Pseudomonas. In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.

Prevalence of R5 and X4-Tropic strains in HIV-1 Infected bangladeshi population

PurposeHIV uses CD4 as main receptor to infect a cell. Also, it uses coreceptor (CCR5 or CXCR4) as a surrogate marker. In Bangladesh, nearly 50% of the identified strains are subtype C. In this study, we have examined viral genotypic co-receptor tropism in Bangladesh People Living with HIV (PLHIV). MethodsWe identified a co-receptor on V3 sequences of the HIV env gene. The online Geno2pheno tools was used. The threshold limit of a 10% false-positive rate was used. Samples from HIV-infected individuals aged 5–50 years were taken from which we obtained a good quality of 55 sequences. The viral tropism frequency in different circulating Bangladeshi HIV subtypes was analyzed using SPSS. ResultsAbove two third of the samples, (61.8%; 34 of 55) were HIV-1 subtype C. We identified 83.6% (46 of 55) of the samples were R5tropic, 16.4% (9 of 55) as X4 tropic, HIV-1 strains. The R5 tropic strains among key population infected with different HIV-1 subtype in the Bangladeshi population is common. ConclusionsThis finding can help with suitable drug selection in reverse-transcriptase (RT) or protease (PR) drug-resistance strains.

Microbiome Analysis of Sugarcane Juices and Biofilms from Louisiana Raw Sugar Factories.

During postharvest processing of sugarcane for raw sugar, microbial activity results in sucrose loss and undesirable exopolysaccharide (EPS) production. Historically, culture-based approaches have focused on the bacterium Leuconostoc mesenteroides as the main contributor to both processes. However, recent studies have shown that diverse microbes are present in sugarcane factories and may also contribute to sugarcane juice deterioration. In the present study, high-throughput amplicon-based sequence profiling was applied to gain a more comprehensive view of the microbial community in Louisiana raw sugar factories. Microbial profiling of the bacterial and fungal microbiomes by 16S V4 and ITS1 sequences, respectively, identified 417 bacterial amplicon sequence variants (ASVs) and 793 fungal ASVs. While Leuconostoc was indeed the most abundant bacterial genus overall (40.9% of 16S sequences), multiple samples were dominated by other taxa such as Weissella and Lactobacillus, underscoring the microbial diversity present in sugarcane factories. Furthermore, flask cultures inoculated with the same samples demonstrated differences in the rate of sucrose consumption, as well as the production of exopolysaccharides and other organic acids, which may result from the observed differences in microbial composition. IMPORTANCE Amplicon-based sequencing was utilized to address long-ignored gaps in microbiological knowledge about the diversity of microbes present in processing streams at Louisiana sugarcane raw sugar factories. These results support an emerging model where diverse organisms contribute to sugarcane juice degradation, help to contextualize microbial contamination problems faced by raw sugar factories, and will guide future studies on biocontrol measures to mitigate sucrose losses and operational challenges due to exopolysaccharide production.