Strong Co-occurrence Research Articles

Gut microbiome: A potential indicator for predicting treatment outcomes in major depressive disorder.

The therapeutic outcomes in major depressive disorder (MDD), one of the most common and heterogeneous mental illnesses, are affected by factors that remain unclear and often yield unsatisfactory results. Herein, we characterized the composition and metabolic function of the gut microbiota of patients with MDD during antidepressant treatment, based on 16S rRNA sequencing and metabolomics. The microbial signatures at baseline differed significantly between responder and non-responder groups. The gut microbiota of the non-responder group was mainly characterized by increased relative abundances of the phylum Actinobacteria, families Christensenellaceae and Eggerthellaceae, and genera Adlercreutzia and Christensenellaceae R7 group compared to that of the responder group. Additionally, the gut microbiota composition of the responder and non-responder groups differed significantly before and after treatment, especially at the genus level. Moreover, 20 differential metabolites between the responder and non-responder groups were identified that were mainly involved in lipid metabolism (cholestane steroids and steroid esters). Eggerthellaceae and Adlercreutzia displayed strong co-occurrence relationships with certain metabolites, suggesting alternations in the gut microbiome, and associated metabolites may be potential mediators of successful antidepressant treatment. Overall, our study demonstrates that alterations in gut microbiota composition and metabolic function might be relevant to the response to antidepressants, thereby providing insight into mechanisms responsible for their efficacy.

Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice

BackgroundMastitis pathogenesis involves a wide range of opportunistic and apparently resident microorganims including bacteria, viruses and archaea. In dairy animals, microbes reside in the host, interact with environment and evade the host immune system, providing a potential for host-tropism to favor mastitis pathogenesis. To understand the host-tropism phenomena of bovine-tropic mastitis microbiomes, we developed a cow-to-mouse mastitis model.MethodsA cow-to-mouse mastitis model was established by fecal microbiota transplantation (FMT) and milk microbiota transplantation (MMT) to pregnant mice to assess microbiome dysbiosis and genomic functional perturbations through shotgun whole metagenome sequencing (WMS) along with histopathological changes in mice mammary gland and colon tissues.ResultsThe cow-to-mouse FMT and MMT from clinical mastitis (CM) cows induced mastitis syndromes in mice as evidenced by histopathological changes in mammary gland and colon tissues. The WMS of 24 samples including six milk (CM = 3, healthy; H = 3), six fecal (CM = 4, H = 2) samples from cows, and six fecal (CM = 4, H = 2) and six mammary tissue (CM = 3, H = 3) samples from mice generating 517.14 million reads (average: 21.55 million reads/sample) mapped to 2191 bacterial, 94 viral and 54 archaeal genomes. The Kruskal–Wallis test revealed significant differences (p = 0.009) in diversity, composition, and relative abundances in microbiomes between CM- and H-metagenomes. These differences in microbiome composition were mostly represented by Pseudomonas aeruginosa, Lactobacillus crispatus, Klebsiella oxytoca, Enterococcus faecalis, Pantoea dispersa in CM-cows (feces and milk), and Muribaculum spp., Duncaniella spp., Muribaculum intestinale, Bifidobacterium animalis, Escherichia coli, Staphylococcus aureus, Massilia oculi, Ralstonia pickettii in CM-mice (feces and mammary tissues). Different species of Clostridia, Bacteroida, Actinobacteria, Flavobacteriia and Betaproteobacteria had a strong co-occurrence and positive correlation as the indicator species of murine mastitis. However, both CM cows and mice shared few mastitis-associated microbial taxa (1.14%) and functional pathways regardless of conservation of mastitis syndromes, indicating the higher discrepancy in mastitis-associated microbiomes among lactating mammals.ConclusionsWe successfully induced mastitis by FMT and MMT that resulted in microbiome dysbiosis and genomic functional perturbations in mice. This study induced mastitis in a mouse model through FMT and MMT, which might be useful for further studies- focused on pathogen(s) involved in mastitis, their cross-talk among themselves and the host.Graphical

Succession and change of potential pathogens in the co-composting of rural sewage sludge and food waste

Composting is an effective way to prevent and control the spread of pathogenic microorganisms which could put potential risk to humans and environment, from rural solid waste, especially sewage sludge and food waste. In the study, we aim to analyze the changes of pathogenic bacteria during the co-composting of rural sewage sludge and food waste. The results showed that only 27 pathogenic bacteria were detected after composting, compared to 50 pathogenic bacteria in the raw mixed pile. About 74% of pathogen concentrations dropped below 1000 copies/g after composting. Lactobacillus, Bacillus, Paenibacillus and Comamonas were the core pathogenic bacteria in the compost, of which concentrations were all significantly lower than that in the raw mixed pile at the end of composting. The concentration of Lactobacillus decreased to 3.03 × 103 copies/g compared to 0 d with 1.25 × 109 copies/g by the end of the composting, while that of Bacillus, Paenibacillus and Comamonas decreased to 2.77 × 104 copies/g, 2.13 × 104 copies/g and 3.38 × 102 copies/g, respectively, with 1.26 × 107 copies/g, 4.71 × 106 copies/g, 1.69 × 108 copies/g on 0 d. Redundancy analysis (RDA) indicated that physicochemical factors and substances could affect the changes of pathogenic bacteria during composting, while temperature was the key influencing factor. In addition, certain potential pathogenic bacteria, such as Bacteroides-Bifidobacterium, show statistically strong and significant co-occurrence during composting, which may increase the risk of multiple infections and also influence their distribution. These findings provide a theoretical reference for biosafety prevention and control in the treatment and disposal of rural solid waste.

Abstract 6148: Immunogenomic landscape of tumor-infiltrating B and plasma cells in early-stage lung adenocarcinoma

Abstract Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths in lifetime smokers. Relative to recent advances in immunotherapy of advanced-stage LUAD, there are very limited strategies for early immune-based treatment or interception of the malignancy in its primitive stages. This is largely due to a poor understanding of the roles and functional phenotypes of distinct immune cell subsets and how they evolve early in LUAD pathogenesis. For instance, while T cells have been a central focus of cancer immunopathology and immunotherapy, the roles of tumor-infiltrating B and plasma cells (TIBs) in the activity of the adaptive immune response along the pathogenic course of solid tumors such as LUAD are extremely poorly understood. To fill these voids, we conducted pan-cancer single-cell RNA sequencing (scRNA-seq) analysis of TIBs using public and in-house cohorts of >15 cancers and matched normal samples. We found that fractions of TIBs, including plasma cells (PCs), were evidently high in the tumor microenvironment (TME) of LUADs, particularly in smokers. We then performed multi-region paired scRNA-seq and single-cell B cell receptor sequencing (scBCR-seq) of tumors and three matched normal lung (NL) tissue samples with varying spatial proximity from each of the tumors of 16 early-stage LUAD patients. Fractions of TIBs including PCs and memory B cells were immensely increased in the TME of early-stage LUADs compared to uninvolved NL, and conversely, the abundance of naïve B cells was markedly decreased. TIB fractions were progressively increased along the pathologic continuum of NL, premalignant lesions (PMLs), up to invasive LUAD. Consistently, expression of the B cell chemotactic CXCL13 - CXCR5 axis in T cells and TIBs, respectively, was increased in both PMLs and LUADs relative to NL. Simultaneous scBCR-seq revealed markedly reduced clonality of BCR repertoires in LUAD compared to NL. Multi-region NL tissues showed progressively increasing BCR clonotype diversity and immunoglobin somatic hypermutation (SHM) with increasing proximity to tumors. BCR clonality was strikingly lower in smoker LUADs relative to non-smoker tumors as well as progressively attenuated with increasing pathologic stage. TIBs in the LUAD TME were mostly composed of terminally differentiated IgA+ or IgG+ PCs and memory B cells with an immunosuppressive phenotype. To understand how TIBs shape the LUAD TME, we also profiled interactions of TIBs with other TME cell components and identified TIB subsets showing strong co-occurrence patterns with immunosuppressive T cell subsets. By comprehensively defining transcriptional profiles, SHM and antibody repertories, as well as cellular interactions of TIBs at single-cell resolution, our results map out the geospatial landscape of TIBs in early-stage LUAD and provide a valuable resource to leverage targets for innovative immunomodulatory strategies. Citation Format: Dapeng Hao, Guangchun Han, Ansam Sinjab, Lorena Gomez Bolanos, Rossana Lazcano Segura, Enyu Dai, Luisa Maren Solis Soto, Edwin Parra, Jennifer Wargo, Stephen Swisher, Tina Cascone, Boris Sepesi, Junya Fujimoto, Steven Dubinett, Ignacio Wistuba, Christopher Stevenson, Avrum Spira, Humam Kadara, Linghua Wang. Immunogenomic landscape of tumor-infiltrating B and plasma cells in early-stage lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6148.

Effects of organic fertilization on functional microbial communities associated with greenhouse gas emissions in paddy soils

Soil microbial communities play a key role in the biochemical processes and nutrient cycles of the soil ecosystem and their byproducts, including greenhouse gases (GHGs). Organic fertilization influences bacterial soil biodiversity and is an essential emission source of GHGs in paddy soil ecosystems. However, the impact of organic fertilization on the functional microorganisms associated with the GHGs methane and nitrous oxide remains unknown. We conducted paddy soil field experiments under three different treatments (no fertilization, base fertilization, and organic fertilization) to investigate the contribution of organic fertilization to soil nutrients and the functional microorganisms associated with GHG emissions. We found that organic fertilization effectively increased the soil organic matter (P < 0.001), soil organic carbon (P < 0.001), and total nitrogen (P < 0.05) as well as the richness (operational taxonomic units and abundance-based coverage estimators) of the methanogenic communities. Correlation analyses showed that methanogenic communities that were present in abundance were more vulnerable to perturbations in soil properties compared to nitrifying bacterial communities. Partial least squares path model analyses elucidated that organic fertilization directly affected both methanogenic communities and nitrifying bacterial communities (P < 0.05), thereby accelerating methane emissions. Strong co-occurrence networks were observed within the soil-dominant phyla Acidobacteria, Bacteroidetes, and Proteobacteria. Our findings highlight the impact of organic fertilization on soil nutrients and functional microorganisms and guide mitigating GHG emissions from paddy soil agroecosystems.

Microbiological Survey of 47 Permanent Makeup Inks Available in the United States.

In two previous surveys, the U.S. Food and Drug Administration (FDA) identified microbial contamination in 53 of 112 (47%) unopened tattoo inks and tattoo-ink-related products (e.g., diluents) from 15 manufacturers in the U.S. In this study, we primarily focused our microbiological survey on permanent makeup (PMU) inks. We conducted a survey of 47 unopened PMU inks from nine manufacturers and a comparative species-centric co-occurrence network (SCN) analysis using the survey results. Aerobic plate count and enrichment culture methods using the FDA’s Bacteriological Analytical Manual (BAM) Chapter 23 revealed that 9 (19%) inks out of 47, from five manufacturers, were contaminated with microorganisms. The level of microbial contamination was less than 250 CFU/g in eight inks and 980 CFU/g in one ink. We identified 26 bacteria that belong to nine genera and 21 species, including some clinically relevant species, such as Alloiococcus otitis, Dermacoccus nishinomiyaensis, Kocuria rosea, and Pasteurella canis. Among the identified microorganisms, the SCN analysis revealed dominance and a strong co-occurrence relation of spore-forming extreme environment survivors, Bacillus spp., with close phylogenetic/phenotypic relationships. These results provide practical insights into the possible microbial contamination factors and positive selection pressure of PMU inks.

Unusual abundance of bloom forming Aulacoseira spp. diatom populations in an anthropogenically impacted stretch of lower part of the River Ganga

The River Ganga is reeling from pressures of rapid urbanization and resulting anthropogenic forcings. In this study, phytoplankton community assemblages were deduced from the Dakshineswar site located in the lower stretch of River Ganga to quantify and understand the health status of this river. Surface water samples were collected from six pre-defined stations of Dakshineswar spanning across monsoon and post-monsoon seasons of 2019 and 2020. Stations were categorized into point source and surface water based on proximity to municipal discharges. Measurement of in situ environmental parameters showed significant differences in values for dissolved oxygen, total dissolved solids, electrical conductivity and suspended particulate matter between the two seasons during the study period. In particular, concentrations of dissolved nitrate and silicate were found to be higher in point source stations compared to surface water stations. The concentration of Chlorophyll-a (Chl-a) was found to be higher in post-monsoon compared to monsoon seasons. Phytoplankton communities consisted of 23 diatom taxa and 14 green algal taxa and they showed distinct seasonal and spatial variations in the study site. Phytoplankton communities were dominated by diatom taxa namely Aulacoseira, Bacillaria, Coscinodiscus, and green algal taxa such as Ulothrix, Chlorella, and Scenedesmus. There was a dramatic increase in cell abundance of Aulacoseira spp. in post-monsoon seasons indicating a bloom-like scenario. Moreover, the rapid increase in cell abundance of Aulacoseira spp. also coincided with an increase in Chl-a and a sharp fall in the concentration of dissolved silicate. Some of the encountered phytoplankton taxa such as Tetraedron, Cosmarium, Nitzschia and Scenedesmus showed strong co-occurrence patterns indicating possible association at ecological scales. Four distinct clusters were formed in nMDS ordination plot based on the influences of environmental variables on encountered phytoplankton taxa. Network analysis revealed evidence of co-occurrence patterns between several diatoms and green algal taxa.

The virota and its transkingdom interactions in the healthy infant gut

SignificanceMicrobes colonizing the infant gut during the first year(s) of life play an important role in immune system development. We show that after birth the (nearly) sterile gut is rapidly colonized by bacteria and their viruses (phages), which often show a strong cooccurrence. Most viruses infecting the infant do not cause clinical signs and their numbers strongly increase after day-care entrance. The infant diet is clearly reflected by identification of plant-infecting viruses, whereas fungi and parasites are not part of a stable gut microbiota. These temporal high-resolution baseline data about the gut colonization process will be valuable for further investigations of pathogenic viruses, dynamics between phages and their bacterial host, as well as studies investigating infants with a disturbed microbiota.

Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue.

Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete nascent chains is poorly understood1,2. Here we uncover Bacillus subtilis MutS2, a member of the conserved MutS family of ATPases that function in DNA mismatch repair3, as an unexpected ribosome-binding protein with an essential function in translational quality control. Cryo-electron microscopy analysis of affinity-purified native complexes shows that MutS2 functions in sensing collisions between stalled and translating ribosomes and suggests how ribosome collisions can serve as platforms to deploy downstream processes: MutS2 has an RNA endonuclease small MutS-related (SMR) domain, as well as an ATPase/clamp domain that is properly positioned to promote ribosomal subunit dissociation, which is a requirement both for ribosome recycling and for initiation of ribosome-associated protein quality control (RQC). Accordingly, MutS2 promotes nascent chain modification with alanine-tail degrons-an early step in RQC-in an ATPase domain-dependent manner. The relevance of these observations is underscored by evidence of strong co-occurrence of MutS2 and RQC genes across bacterial phyla. Overall, the findings demonstrate a deeply conserved role for ribosome collisions in mounting a complex response to the interruption of translation within open reading frames.

Continuity of Psychopathology Throughout Adolescence and Young Adulthood

ABSTRACT Objective This study tested two opposing hypotheses on the continuity of psychopathology throughout adolescence and young adulthood; differentiation versus dynamic mutualism. Differentiation predicts that co-occurrence decreases, while dynamic mutualism predicts that co-occurrence increases due to causal interactions amongst mental health problems. Method Using data from the Dutch TRacking Adolescents’ Individual Lives Survey (n = 2228, 51% female), we studied the development of self-reported internalizing, externalizing, and attention problems at ages 11 to 26 across six waves. Random-intercept cross-lagged panel modeling was employed to distinguish within-person development from stable between-person processes. Results Large stable between-person associations indicated that adolescents with internalizing problems tended to have both externalizing and attention problems as well. On a within-person level, mental health problems showed partial stability and strong cross-sectional co-occurrence. Within-wave associations of internalizing with externalizing or attention problems decreased between age 11 and 16 years, after which they increased again. Little heterotypic continuity was found: age 11 externalizing predicted age 13 attention, which in turn predicted age 16 externalizing problems, and internalizing predicted externalizing problems across ages 22 to 26. Findings were similar for males and females. Conclusions Our findings suggest co-occurrence decreases during early and middle adolescence, supporting differentiation. While co-occurrence increased again into young adulthood, this could not be labeled as dynamic mutualism because little evidence for heterotypic continuity was found in this phase of life. The strong stable links between internalizing, externalizing, and attention problems stress the importance of targeting these mental health problems and their shared risk factors together.

Slope aspect determines the abundance and composition of nitrogen‐cycling microbial communities in an alpine ecosystem

Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning.

Intervalley Excitonic Hybridization, Optical Selection Rules, and Imperfect Circular Dichroism in Monolayer h-BN.

We perform first-principles GW plus Bethe-Salpeter equation calculations to investigate the photophysics of monolayer hexagonal boron nitride (h-BN), revealing excitons with novel k-space characteristics. The excitonic states forming the first and third peaks in its absorption spectrum are s-like, but those of the second peak are notably p-like, a first finding of strong co-occurrence of bright s-like and bright p-like states in an intrinsic 2D material. Moreover, even though the k-space wave function of these excitonic states are centered at the K and K^{'} valleys as in monolayer transition metal dichalcogenides, the k-space envelope functions of the basis excitons at one valley have significant extents to the basin of the other valley. As a consequence, the optical response of monolayer h-BN exhibits a lack of circular dichroism, as well as a coupling that induces an intervalley mixing between s- and p-like states.

Seroreactivity Against Tyrosine Phosphatase PTPRN Links Type 2 Diabetes and Colorectal Cancer and Identifies a Potential Diagnostic and Therapeutic Target.

Colorectal cancer (CRC) and diabetes are two of the most prevalent chronic diseases worldwide with dysregulated receptor tyrosine kinase signaling and strong co-occurrence correlation. Plasma autoantibodies represent a promising early diagnostic marker for both diseases before symptoms appear. In this study, we explore the value of autoantibodies against receptor-type tyrosine-protein phosphatase-like N (PTPRN; full-length or selected domains) as diagnostic markers using a cohort of individuals with type 2 diabetes (T2D), CRC, or both diseases or healthy individuals. We show that PTPRN autoantibody levels in plasma discriminated between patients with T2D with and without CRC. Consistently, high PTPRN expression correlated with decreased survival of patients with CRC. Mechanistically, PTPRN depletion significantly reduced invasiveness of CRC cells in vitro and liver homing and metastasis in vivo by means of a dysregulation of the epithelial-mesenchymal transition and a decrease of the insulin receptor signaling pathway. Therefore, PTPRN autoantibodies may represent a particularly helpful marker for the stratification of patients with T2D at high risk of developing CRC. Consistent with the critical role played by tyrosine kinases in diabetes and tumor biology, we provide evidence that tyrosine phosphatases such as PTPRN may hold potential as therapeutic targets in patients with CRC.

Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake

The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments’ physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.

Discovering disease\u2013disease associations using electronic health records in The Guideline Advantage (TGA) dataset

Certain diseases have strong comorbidity and co-occurrence with others. Understanding disease–disease associations can potentially increase awareness among healthcare providers of co-occurring conditions and facilitate earlier diagnosis, prevention and treatment of patients. In this study, we utilized the valuable and large The Guideline Advantage (TGA) longitudinal electronic health record dataset from 70 outpatient clinics across the United States to investigate potential disease–disease associations. Specifically, the most prevalent 50 disease diagnoses were manually identified from 165,732 unique patients. To investigate the co-occurrence or dependency associations among the 50 diseases, the categorical disease terms were first mapped into numerical vectors based on disease co-occurrence frequency in individual patients using the Word2Vec approach. Then the novel and interesting disease association clusters were identified using correlation and clustering analyses in the numerical space. Moreover, the distribution of time delay (Δt) between pair-wise strongly associated diseases (correlation coefficients ≥ 0.5) were calculated to show the dependency among the diseases. The results can indicate the risk of disease comorbidity and complications, and facilitate disease prevention and optimal treatment decision-making.

O-129 Lactobacillus deplete vaginal microbial composition is associated with chromosomally normal miscarriage and local inflammation

Abstract Study question To investigate the vaginal microbial composition and the local immune response in chromosomally normal and abnormal miscarriages and compare this to uncomplicated pregnancies delivering at term. Summary answer We show that euploid miscarriage is associated with a significantly higher prevalence of Lactobacillus spp. deplete vaginal microbial communities compared to aneuploid miscarriage. What is known already Emerging evidence supports the role of the vaginal microbiota in adverse pregnancy outcome, but the underlying mechanisms are poorly understood. A dominance of Lactobacillus spp. in pregnancy provides protection against pathogenic bacteria by producing lactic acid and antimicrobial compounds. A depletion in Lactobacillus spp. is often linked to adverse pregnancy outcomes.Current work also implicates the reproductive tract microbiota as a key modulator of local inflammatory and immune pathways. We have previously shown that miscarriage is associated with vaginal dysbiosis but without knowledge of the cytogenetic status of those miscarriages or the local immune profile. Study design, size, duration This study was a prospective observational cohort study based at Queen Charlotte’s &amp; Chelsea Hospital, Early Pregnancy Unit, London between March 2014-February 2019. Vaginal swabs were collected from the posterior vaginal fornix of 167 patients. Participants/materials, setting, methods We used 16S rRNA gene based metataxonomics to interrogate the vaginal microbiota in a cohort of 167 women, 93 miscarriage patients (54 euploid and 39 aneuploid using molecular cytogenetics) and 74 women who delivered at term and correlate this with the aneuploidy status of the miscarriages. We also measured the concentrations of IL-2, IL-4, IL-6, IL-8, TNF-α, IFN-γ, IL-1β, IL-18 and IL-10 in cervical vaginal fluid using Human Magnetic Luminex Screening Assay (8-plex). Main results and the role of chance We show that euploid miscarriage is associated with a significantly higher prevalence of Lactobacillus spp. deplete vaginal microbial communities compared to aneuploid miscarriage (P=0.008). In women having Lactobacillus spp. deplete vaginal microbial communities, euploid miscarriage associates with higher concentrations of pro-inflammatory cytokines IL-1β, IL-8, IL-6 (P&amp;lt;0.001, P=0.01 and P&amp;lt;0.001 respectively) and lower concentrations of anti-inflammatory cytokines IL10 (P&amp;lt;0.001) when compared to viable term pregnancy. We identified Prevotella bivia and Streptococcus as particularly common in euploid miscarriage and as drivers of pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α). Co-occurrence network analyses revealed low levels of co-occurrence between Lactobacillus crispatus and other organisms and strong co-occurrence between Streptococcal species. Our data show a combination of both an adverse vaginal microbiota and a cytokine response to it influences early pregnancy outcome. Although this may be a reflection of intrinsic maternal immune response, it appears that the cytokine response is largely driven by the bacterial taxa present in the vagina, which presents an opportunity for specific, directed intervention. The negative co-occurrence between L.crispatus and all other organisms suggests a possible therapeutic role for probiotics containing this organism. The influence of Streptococci also suggests a potential benefit of targeted antibiotics with probiotics for some patients. Limitations, reasons for caution There were no longitudinal samples in this cohort and our results are based on the assumption that the vaginal microbial composition is stable throughout the first trimester.Future longitudinal studies with larger sample sizes are needed to corroborate these findings and provide insights to the mechanisms that trigger the inflammatory response. Wider implications of the findings These findings support the hypothesis that the vaginal microbiota plays an important aetiological role in euploid miscarriage and may represent a target to modify the risk of pregnancy loss. Trial registration number n/a

Metagenomic profiles and health risks of pathogens and antibiotic resistance genes in various industrial wastewaters and the associated receiving surface water

The aquatic environment may represent an essential route for transmission of antibiotic resistance to opportunistic human pathogens. Since industrial wastewater is discharged into the river after treatment, understanding the distribution of antibiotic resistance genes (ARGs) in river systems and the possibility of pathogens acquiring antibiotic resistance are challenges with far-reaching significance. This work mainly studied distribution profiles of pathogens and ARGs, and compared their health risk in various industrial wastewater with that of river water. Results showed that 166 pathogens were concurrently shared by the six water samples, with Salmonella enterica and Pseudomonas aeruginosa being the most abundant, followed by Fusarium graminearum and Magnaporthe oryzae. The similar composition of the pathogens suggests that pathogens in river water may mainly come from sewage discharge of slaughterhouses and that changes in water quality contribute significantly to the prevalence of these pathogens. Of the 57 ARG types detected, bacitracin was the most abundant, followed by sulfonamide, chloramphenicol, tetracycline, and aminoglycoside. Strikingly, the wastewater from a pharmaceutical factory producing Chinese medicine was also rich in bacA, sul1, mexW, mexB, mexF and oprn. It can be seen from the co-occurrence patterns that pathogens and the main ARGs have strong co-occurrence. Higher abundance of offensive virulence factors in industrial wastewater and their strong correlation with pathogens containing ARGs suggest higher microbiological risk. These findings highlight the need to assess ARG acquisition by pathogens in the surface water of human-impacted environments where pathogens and ARGs may co-thrive.

Collocates of 'great' and 'good' in the Corpus of Contemporary American English and Indonesian EFL textbooks

Previous studies have proven some discrepancies between language presented in EFL textbooks and the real use of English. This fact contradicts the teaching materials’ aim, which is intended to equip the learners to be communicatively competent. This study then investigates the use of adjectives, limited to ‘great’ and ‘good’ in terms of the frequent and strong co-occurrences, i.e., collocations, in a general reference corpus of Standard English to be compared with those in Indonesian EFL textbooks. The data were collected from both the corpus and the textbooks, but the analyses in the textbooks were generated based on the Mutual Information (MI) score of the collocates. Based on the comparison, it is evident that there are some similarities between adjective use in the textbooks and the corpus in terms of verb collocates of the adjectives. The mismatches, however, are quite remarkable, especially in terms of the variability of adverb collocates and the absence of prominent noun collocates in the textbooks. Pedagogically speaking, these results should be taken into consideration in writing the textbooks to enhance the quality of the language content prepared for the learners in the EFL context.

The emergence of residential satisfaction studies in social research: A bibliometric analysis

This research aims to review the total collection of literature on the ‘residential satisfaction’ concept used in social research from 1961 to 2020, and provides a complete overview on how social research concerning ‘residential satisfaction’ has emerged and developed in the last 60 years. We follow the theoretical framework of bibliometric analysis and use the bibliometric datasets retrieved from Web of Science and Scopus's online resources. After compiling and processing the datasets, we used a final dataset containing 877 documents on residential satisfaction. The open-source statistical and visualisation software packages R and VOSviewer were used mainly for processing and analysing datasets. The results visualise information on the top authors, the most influential documents by citation, the most productive countries, and other criteria. The lexical network analysis shows that residential satisfaction has a strong co-occurrence association with the two frequently occurring terms ‘neighbourhood’ and ‘satisfaction’. The majority of research on residential satisfaction has been conducted in the United States, China, and the United Kingdom. The top three most influential journals for residential satisfaction research are ‘Social Indicators Research’, ‘Environment and Development’, and ‘Habitat International’. This bibliometric analysis frames the future research demand for residential satisfaction in social research.

The diversity and function of sourdough starter microbiomes.

Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.