DADA2: High-resolution sample inference from Illumina amplicon data

Biomimetic nanoplatform with microbiome modulation and antioxidant functions ameliorating insulin resistance and pancreatic β-cell dysfunction for T2DM management

Insulin resistance and pancreatic β-cell dysfunction are the main pathogenesis of type 2 diabetes mellitus (T2DM). However, insulin therapy and diabetes medications do not effectively solve the two problems simultaneously. In this study, a biomimetic oral hydrogen nanogenerator that leverages the benefits of edible plant-derived exosomes and hydrogen therapy was constructed to overcome this dilemma by modulating gut microbiota and ameliorating oxidative stress and inflammatory responses. Hollow mesoporous silica (HMS) nanoparticles encapsulating ammonia borane (A) were used to overcome the inefficiency of H2 delivery in traditional hydrogen therapy, and exosomes originating from ginger (GE) were employed to enhance biocompatibility and regulate intestinal flora. Our study showed that HMS/A@GE not only considerably ameliorated insulin resistance and liver steatosis, but inhibited the dedifferentiation of islet β-cell and enhanced pancreatic β-cell proportion in T2DM model mice. In addition to its antioxidant and anti-inflammatory effects, HMS/A@GE augmented the abundance of Lactobacilli spp. and tryptophan metabolites, such as indole and indole acetic acid, which further activated the AhR/IL-22 pathway to improve intestinal-barrier function and metabolic impairments. This study offers a potentially viable strategy for addressing the current limitations of diabetes treatment by integrating gut-microbiota remodelling with antioxidant therapies.

Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis: Effect of the carbon source and SIFT-MS method development

The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation strategies. In this study, we evaluated the removal of a gaseous mixture containing toluene, m-xylene, ethylbenzene, cyclohexane, butane, pentane, hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile conditions. For the real-time measurement of hydrocarbons, a novel systematic approach was implemented using Selected-Ion Flow Tube Mass Spectrometry (SIFT-MS). The effect of the carbon source (∼9.5 ppmv) on (i) the bioreactors' performance (BR1: dosed with only cyclohexane as a single hydrocarbon versus BR2: dosed with a mixture of the 8 hydrocarbons) and (ii) the evolution of microbial communities over time were investigated. The results showed that cyclohexane reached a maximum removal efficiency (RE) of 53% ± 4% in BR1. In BR2, almost complete removal of toluene, m-xylene and ethylbenzene, being the most water-soluble and easy-to-degrade carbon sources, was observed. REs below 32% were obtained for the remaining compounds. By exposing the microbial consortium to only the five most recalcitrant hydrocarbons, REs between 45% ± 5% and 98% ± 1% were reached. In addition, we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities developed. The abundance of species belonging to the genus Rhodococcus was below 10% in all bioreactors at the end of the experiments. This work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors, along with a systematic approach for the development of SIFT-MS methods.

Enhancing microbial superoxide generation and conversion to hydroxyl radicals for enhanced bioremediation using iron-binding ligands

Harnessing bacteria for superoxide production in bioremediation holds immense promise, yet its practical application is hindered by slow production rates and the relatively weak redox potential of superoxide. This study delves into a cost-effective approach to amplify superoxide production using an Arthrobacter strain, a prevalent soil bacterial genus. Our research reveals that introducing a carbon source along with specific iron-binding ligands, including deferoxamine (DFO), diethylenetriamine pentaacetate (DTPA), citrate, and oxalate, robustly augments microbial superoxide generation. Moreover, our findings suggest that these iron-binding ligands play a pivotal role in converting superoxide into hydroxyl radicals by modulating the electron transfer rate between Fe(III)/Fe(II) and superoxide. Remarkably, among the tested ligands, only DTPA emerges as a potent promoter of this conversion process when complexed with Fe(III). We identify an optimal Fe(III) to DTPA ratio of approximately 1:1 for enhancing hydroxyl radical production within the Arthrobacter culture. This research underscores the efficacy of simultaneously introducing carbon sources and DTPA in facilitating superoxide production and its subsequent conversion to hydroxyl radicals, significantly elevating bioremediation performance. Furthermore, our study reveals that DTPA augments superoxide production in cultures of diverse soils, with various soil microorganisms beyond Arthrobacter identified as contributors to superoxide generation. This emphasizes the universal applicability of DTPA across multiple bacterial genera. In conclusion, our study introduces a promising methodology for enhancing microbial superoxide production and its conversion into hydroxyl radicals. These findings hold substantial implications for the deployment of microbial reactive oxygen species in bioremediation, offering innovative solutions for addressing environmental contamination challenges.

Functional and structural responses of a halophilic consortium to oily sludge during biodegradation

Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C10-C30) fraction of the oily sludge within 7 days in the presence of 100 g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl2, MgCl2, CaCl2, trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16 S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation.

Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems

Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.

Explainable machine learning model for identifying key gut microbes and metabolites biomarkers associated with myasthenia gravis

Diagnostic markers for myasthenia gravis (MG) are limited; thus, innovative approaches are required for supportive diagnosis and personalized care. Gut microbes are associated with MG pathogenesis; however, few studies have adopted machine learning (ML) to identify the associations among MG, gut microbiota, and metabolites. In this study, we developed an explainable ML model to predict biomarkers for MG diagnosis. We enrolled 19 MG patients and 10 non-MG individuals. Stool samples were collected and microbiome assessment was performed using 16S rRNA sequencing. Untargeted metabolic profiling was conducted to identify fecal amplicon significant variants (ASVs) and metabolites. We developed an explainable ML model in which the top ASVs and metabolites are combined to identify the best predictive performance. This model uses the SHapley Additive exPlanations method to generate both global and personalized explanations. Fecal microbe-metabolite composition differed significantly between groups. The key bacterial families were Lachnospiraceae and Ruminococcaceae, and the top three features were Lachnospiraceae, inosine, and methylhistidine. An ML model trained with the top 1 % ASVs and top 15 % metabolites combined outperformed all other models. Personalized explanations revealed different patterns of microbe-metabolite contributions in patients with MG. The integration of the microbiota-metabolite features and the development of an explainable ML framework can accurately identify MG and provide personalized explanations, revealing the associations between gut microbiota, metabolites, and MG. An online calculator employing this algorithm was developed that provides a streamlined interface for MG diagnosis screening and conducting personalized evaluations.

"Active carbon" is more advantageous to the bacterial community in the rice rhizosphere than "stable carbon"

Carbon materials are commonly used for soil carbon sequestration and fertilization, which can also affect crop growth by manipulating the rhizosphere bacterial community. However, the comparison of the differences between active carbon (e.g., organic fertilizers) and stable carbon (e.g., biochar) on rhizosphere microdomains is still unclear. Hence, a trial was implemented to explore the influence of control (CK, no fertilizer; NPK, chemical fertilizer), organic fertilizer (CF-O, organic fertilizer; CF-BO, biochar-based organic fertilizer) and biochar material (CF-B, perishable garbage biochar; CF-PMB, pig manure biochar) on the diversity, composition, and interaction of rice rhizosphere bacterial community through 16 S rRNA gene high-throughput sequencing. Our results demonstrate that organic fertilizer increases bacterial alpha-diversity compared to no-carbon supply treatment to the extend, whereas biochar has the opposite effect. The rhizosphere bacterial community composition showed pronounced variations among the various fertilization treatments. The relative abundance in Firmicutes decreased with organic fertilizer application, whereas that in Chloroflexi and Actinobacteria decreased with biochar application. Bacterial network analysis demonstrate that organic fertilizer enhances the complexity and key taxa of bacterial interactions, while biochar exhibits an opposing trend. The findings of our study indicate that organic fertilizer may contribute to a positive and advantageous impact on bacterial diversity and interaction in rice rhizosphere, whereas the influence of biochar is not as favorable and constructive. This study lays the foundation for elucidating the fate of the rhizosphere bacterial community following different carbon material inputs in the context of sustainable agricultural development.

Canagliflozin attenuates kidney injury, gut-derived toxins, and gut microbiota imbalance in high-salt diet-fed Dahl salt-sensitive rats

PURPOSE

To investigate the effects of canagliflozin (20 mg/kg) on Dahl salt-sensitive (DSS) rat gut microbiota and salt-sensitive hypertension-induced kidney injury and further explore its possible mechanism.

METHODS

Rats were fed a high-salt diet to induce hypertension and kidney injury, and physical and physiological indicators were measured afterwards. This study employed 16S rRNA sequencing technology and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolic profiling combined with advanced differential and association analyses to investigate the correlation between the microbiome and the metabolome in male DSS rats.

RESULTS

A high-salt diet disrupted the balance of the intestinal flora and increased toxic metabolites (methyhistidines, creatinine, homocitrulline, and indoxyl sulfate), resulting in severe kidney damage. Canagliflozin contributed to reconstructing the intestinal flora of DSS rats by significantly increasing the abundance of Corynebacterium spp., Bifidobacterium spp., Facklamia spp., Lactobacillus spp., Ruminococcus spp., Blautia spp., Coprococcus spp., and Allobaculum spp. Moreover, the reconstruction of the intestinal microbiota led to significant changes in host amino acid metabolite concentrations. The concentration of uremic toxins, such as methyhistidines, creatinine, and homocitrulline, in the serum of rats was decreased by canagliflozin, which resulted in oxidative stress and renal injury alleviation.

CONCLUSION

Canagliflozin may change the production of metabolites and reduce the level of uremic toxins in the blood circulation by reconstructing the intestinal flora of DSS rats fed a high-salt diet, ultimately alleviating oxidative stress and renal injury.

Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis

The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.

Disturbance of the human gut microbiota in patients with Myotonic Dystrophy type 1

Myotonic dystrophy type 1 (DM1) is a rare autosomal dominant genetic disorder. Although DM1 is primarily characterized by progressive muscular weakness, it exhibits many multisystemic manifestations, such as cognitive deficits, cardiac conduction abnormalities, and cataracts, as well as endocrine and reproductive issues. Additionally, the gastrointestinal (GI) tract is frequently affected, encompassing the entire digestive tract. However, the underlying causes of these GI symptoms remain uncertain, whether it is biomechanical problems of the intestine, involvement of bacterial communities, or both. The primary objective of this study is to investigate the structural changes in the gut microbiome of DM1 patients. To achieve this purpose, 35 patients with DM1 were recruited from the DM-Scope registry of the neuromuscular clinic in the Saguenay-Lac-St-Jean region of the province of Québec, Canada. Stool samples from these 35 patients, including 15 paired samples with family members living with them as controls, were collected. Subsequently, these samples were sequenced by 16S MiSeq and were analyzed with DADA2 to generate taxonomic signatures. Our analysis revealed that the DM1 status correlated with changes in gut bacterial community. Notably, there were differences in the relative abundance of Bacteroidota, Euryarchaeota, Fusobacteriota, and Cyanobacteria Phyla compared to healthy controls. However, no significant shift in gut microbiome community structure was observed between DM1 phenotypes. These findings provide valuable insights into how the gut bacterial community, in conjunction with biomechanical factors, could potentially influence the gastrointestinal tract of DM1 patients.

A disturbed metabolite-GPCR axis is associated with microbial dysbiosis in IBD patients: Potential role of GPR109A in macrophages

Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by disrupted immune function. Indeed, gut microbiota dysbiosis and metabolomic profile alterations, are hallmarks of IBD. In this scenario, metabolite-sensing G-protein coupled receptors (GPCRs), involved in several biological processes, have emerged as pivotal players in the pathophysiology of IBD. The aim of this study was to characterize the axis microbiota-metabolite-GPCR in intestinal surgical resections from IBD patients. Results showed that UC patients had a lower microbiota richness and bacterial load, with a higher proportion of the genus Cellulosimicrobium and a reduced proportion of Escherichia, whereas CD patients showed a decreased abundance of Enterococcus. Furthermore, metabolomic analysis revealed alterations in carboxylic acids, fatty acids, and amino acids in UC and CD samples. These patients also exhibited upregulated expression of most metabolite-sensing GPCRs analysed, which positively correlated with pro-inflammatory and pro-fibrotic markers. The role of GPR109A was studied in depth and increased expression of this receptor was detected in epithelial cells and cells from lamina propria, including CD68+ macrophages, in IBD patients. The treatment with β-hydroxybutyrate increased gene expression of GPR109A, CD86, IL1B and NOS2 in U937-derived macrophages. Besides, when GPR109A was transiently silenced, the mRNA expression and secretion of IL-1β, IL-6 and TNF-α were impaired in M1 macrophages. Finally, the secretome from siGPR109A M1 macrophages reduced the gene and protein expression of COL1A1 and COL3A1 in intestinal fibroblasts. A better understanding of metabolite-sensing GPCRs, such as GPR109A, could establish their potential as therapeutic targets for managing IBD.

Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma

Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). Fecal specimens were obtained from 16 healthy controls, 33 patients with viral-HCC (17 and 16 cases with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, respectively), and 18 patients with NBNC-HCC. Compositions of fecal microbiota were assessed by 16S rRNA sequencing. Bioinformatic analysis was performed by the DADA2 pipeline in the R program. Significantly different genera from the top 50 relative abundance were used to classify between subgroups of HCC by the Random Forest algorithm. Our data demonstrated that the HCC group had a significantly decreased alpha-diversity and changed microbial composition in comparison with healthy controls. Within the top 50 relative abundance, there were 11 genera including Faecalibacterium, Agathobacter, and Coprococcus that were significantly enhanced in Viral-HCC, while 5 genera such as Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium were enhanced in NBNC-HCC. Compared to Viral-HCC, the NBNC-HCC subgroup significantly reduced various short-chain fatty acid-producing bacteria, as well as declined fecal butyrate but elevated plasma surrogate markers of microbial translocation. Based on the machine learning algorithm, a high diagnostic accuracy to classify HCC subgroups was achieved with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.94. Collectively, these data revealed that gut dysbiosis was distinct according to etiological factors of HCC, which might play an essential role in hepatocarcinogenesis. These findings underscore the possible use of a gut microbiota signature for the diagnosis and therapeutic approaches regarding different subgroups of HCC. KEY POINTS: • Gut dysbiosis is connected to hepatocarcinogenesis and can be used as a novel biomarker. • Gut microbiota composition is significantly altered in different etiological factors of HCC. • Microbiota-based signature can accurately distinguish between Viral-HCC and NBNC-HCC.

Effects of age on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks by 16 S and transcriptomics

Duck hepatitis A virus genotype 3 (DHAV-3) is the major cause of viral hepatitis in ducks in Asia. Previous studies have shown that ducklings younger than 21 days are more susceptible to DHAV-3. To elucidate the mechanism by which age affects the differential susceptibility of Pekin ducks to DHAV-3, intestinal (n = 520), liver (n = 40) and blood (n = 260) samples were collected from control and DHAV-3-infected ducks at 7, 10, 14, and 21 days of age. Comparisons of plasma markers, mortality rates, and intestinal histopathological data showed that the resistance of Pekin ducks to DHAV-3 varied with age. 16 S sequencing revealed that the ileal microbial composition was influenced by age, and this correlation was greater than that recorded for caecal microbes. Candidatus Arthromitus, Bacteroides, Corynebacterium, Enterococcus, Romboutsia, and Streptococcus were the differntially abundant microbes in the ileum at the genus level after DHAV-3 infection and were significantly correlated with 7 differentially expressed genes (DEGs) in 7- and 21-day-old ducklings. 3 immunity-related pathways were significantly different between 7- and 21-day-old ducklings, especially for IFIH1-mediated induction of the interferon-alpha/beta pathway, which induces differential production of CD8(+) T cells and was influenced by a combination of differentially abundant microbiota and DEGs. We found that microbes in the ileum changed regularly with age. The intestinal microbiota was associated with the expression of genes in the liver through IFIH1-mediated induction of the interferon-alpha/beta pathway, which may partially explain why younger ducklings were more susceptible to DHAV-3 infection.

Role of folic acid in regulating gut microbiota and short-chain fatty acids based on an in vitro fermentation model

Folic acid deficiency is common worldwide and is linked to an imbalance in gut microbiota. However, based on model animals used to study the utilization of folic acid by gut microbes, there are challenges of reproducibility and individual differences. In this study, an in vitro fecal slurry culture model of folic acid deficiency was established to investigate the effects of supplementation with 5-methyltetrahydrofolate (MTHF) and non-reduced folic acid (FA) on the modulation of gut microbiota. 16S rRNA sequencing results revealed that both FA (29.7%) and MTHF (27.9%) supplementation significantly reduced the relative abundance of Bacteroidetes compared with control case (34.3%). MTHF supplementation significantly improved the relative abundance of Firmicutes by 4.49%. Notably, compared with the control case, FA and MTHF supplementation promoted an increase in fecal levels of Lactobacillus, Bifidobacterium, and Pediococcus. Short-chain fatty acid (SCFA) analysis showed that folic acid supplementation decreased acetate levels and increased fermentative production of isobutyric acid. The in vitro fecal slurry culture model developed in this study can be utilized as a model of folic acid deficiency in humans to study the gut microbiota and demonstrate that exogenous folic acid affects the composition of the gut microbiota and the level of SCFAs. KEY POINTS: • Establishment of folic acid deficiency in an in vitro culture model. • Folic acid supplementation regulates intestinal microbes and SCFAs. • Connections between microbes and SCFAs after adding folic acid are built.

Molecular analysis of feces reveals gastrointestinal nematodes in reintroduced wild asses of the Negev desert

Reintroduced animals face disease risks, potentially impacting both the reintroduced and the local wildlife/domestic populations. This study focuses on the Asiatic wild asses (Equus hemionus) reintroduced to the Negev desert in southern Israel. Despite potential threats of disease spill-over to and from domesticated donkeys and horses in the area, there are no records of the gastrointestinal nematodes (GIN) of the wild ass population. We used DNA metabarcoding on fecal samples of wild asses collected across seasons and habitats, near water sources that they frequently use. Ten GIN species were detected in the feces, nine belonging to the family Strongylidae, which commonly infects and causes disease in equids worldwide, such as horses, zebras, and donkeys. Some of these Strongylidae species are also found in domesticated equids in Israel, thus raising concerns regarding potential parasite transmission between wild and domestic animals. The high prevalence of certain GIN species suggests frequent transmission, likely due to the congregation of the wild asses around water sources. While we observed statistically significant variations in some GIN species across seasons and habitats, we did not find clear overall differences between GIN communities. DNA metabarcoding proves to be a valuable tool for identifying GIN species in wild animals, with potential applications in monitoring their health and preventing disease transmission to and from domestic animals.

Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease

INTRODUCTION

A large proportion of patients with inflammatory bowel disease (IBD) experience IBD-related inflammatory conditions outside of the gastrointestinal tract, termed extraintestinal manifestations (EIMs) which further decreases quality of life and, in extreme cases, can be life threatening. The pathogenesis of EIMs remains unknown, and although gut microbiota alterations are a well-known characteristic of patients with IBD, its relationship with EIMs remains sparsely investigated. This study aimed to compare the gut microbiota of patients with IBD with and without EIMs.

METHODS

A total of 131 Danish patients with IBD were included in the study, of whom 86 had a history of EIMs (IBD-EIM) and 45 did not (IBD-C). Stool samples underwent 16S rRNA sequencing. Amplicon sequence variants (ASVs) were mapped to the Silva database. Diversity indices and distance matrices were compared between IBD-EIM and IBD-C. Differentially abundant ASVs were identified using a custom multiple model statistical analysis approach, and modules of co-associated bacteria were identified using sparse correlations for compositional data (SparCC) and related to patient EIM status.

RESULTS

Patients with IBD and EIMs exhibited increased disease activity, body mass index, increased fecal calprotectin levels and circulating monocytes and neutrophils. Microbiologically, IBD-EIM exhibited lower fecal microbial diversity than IBD-C (Mann-Whitney's test, p = .01) and distinct fecal microbiota composition (permutational multivariate analysis of variance; weighted UniFrac, R2 = 0.018, p = .01). A total of 26 ASVs exhibited differential relative abundances between IBD-EIM and IBD-C, including decreased Agathobacter and Blautia and increased Eggerthella lenta in the IBD-EIM group. SparCC analysis identified 27 bacterial co-association modules, three of which were negatively related to EIM (logistic regression, p < .05) and included important health-associated bacteria, such as Agathobacter and Faecalibacterium.

CONCLUSIONS

The fecal microbiota in IBD patients with EIMs is distinct from that in IBD patients without EIM and could be important for EIM pathogenesis.

Response of particle-attached and free-living bacterial communities to Microcystis blooms

The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.

Large intestinal nutritional and physicochemical parameters from different dog sizes reshape canine microbiota structure and functions in vitro

Different dog sizes are associated with variations in large intestinal physiology including gut microbiota, which plays a key role in animal health. This study aims to evaluate, using the CANIM-ARCOL (Canine Mucosal Artificial Colon), the relative importance of gut microbes versus physicochemical and nutritional parameters of the canine colonic environment in shaping microbiota structure and functions. CANIM-ARCOL was set up to reproduce nutrient availability, bile acid profiles, colonic pH, and transit time from small, medium, or large dogs according to in vivo data, while bioreactors were all inoculated with a fecal sample collected from medium size dogs (n = 2). Applying different dog size parameters resulted in a positive association between size and gas or SCFA production, as well as distinct microbiota profiles as revealed by 16S Metabarcoding. Comparisons with in vivo data from canine stools and previous in vitro results obtained when CANIM-ARCOL was inoculated with fecal samples from three dog sizes revealed that environmental colonic parameters were sufficient to drive microbiota functions. However, size-related fecal microbes were necessary to accurately reproduce in vitro the colonic ecosystem of small, medium, and large dogs. For the first time, this study provides mechanistic insights on which parameters from colonic ecosystem mainly drive canine microbiota in relation to dog size. The CANIM-ARCOL can be used as a relevant in vitro platform to unravel interactions between food or pharma compounds and canine colonic microbiota, under different dog size conditions. The potential of the model will be extended soon to diseased situations (e.g. chronic enteropathies or obesity).

Probiotic therapy modulates the brain-gut-liver microbiota axis in a mouse model of traumatic brain injury

The interplay between gut microbiota and host health is crucial for maintaining the overall health of the body and brain, and it is even more crucial how changes in the bacterial profile can influence the aftermath of traumatic brain injury (TBI). We studied the effects of probiotic treatment after TBI to identify potential changes in hepatic lipid species relevant to brain function. Bioinformatic analysis of the gut microbiota indicated a significant increase in the Firmicutes/Bacteroidetes ratio in the probiotic-treated TBI group compared to sham and untreated TBI groups. Although strong correlations between gut bacteria and hepatic lipids were found in sham mice, TBI disrupted these links, and probiotic treatment did not fully restore them. Probiotic treatment influenced systemic glucose metabolism, suggesting altered metabolic regulation. Behavioral tests confirmed memory improvement in probiotic-treated TBI mice. While TBI reduced hippocampal mRNA expression of CaMKII and CREB, probiotics reversed these effects yet did not alter BDNF mRNA levels. Elevated pro-inflammatory markers TNF-α and IL1-β in TBI mice were not significantly affected by probiotic treatment, pointing to different mechanisms underlying the probiotic benefits. In summary, our study suggests that TBI induces dysbiosis, alters hepatic lipid profiles, and preemptive administration of Lactobacillus helveticus and Bifidobacterium longum probiotics can counter neuroplasticity deficits and memory impairment. Altogether, these findings highlight the potential of probiotics for attenuating TBI's detrimental cognitive and metabolic effects through gut microbiome modulation and hepatic lipidomic alteration, laying the groundwork for probiotics as a potential TBI therapy.

Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae)

Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.

Shifts in the microbial community and metabolome in rumen ecological niches during antler growth

Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.

Liposome-based RNAi delivery in honeybee for inhibiting parasite Nosema ceranae

Nosema ceranae, a parasite that parasitizes and reproduces in the gut of honeybees, has become a serious threat to the global apiculture industry. RNA interference (RNAi) technology can be used to inhibit N. ceranae growth by targeting silencing the thioredoxin reductase (TrxR) in N. ceranae. However, suitable carriers are one of the reasons limiting the application of RNAi due to the easy degradation of dsRNA in honeybees. As a vesicle composed of a lipid bilayer, liposomes are a good carrier for nucleic acid delivery, but studies in honeybees are lacking. In this study, liposomes were used for double-stranded RNA (dsRNA) dsTrxR delivery triggering RNAi to inhibit the N. ceranae growth in honeybees. Compared to naked dsTrxR, liposome-dsTrxR reduced N. ceranae numbers in the midgut and partially restored midgut morphology without affecting bee survival and gut microbial composition. The results of this study confirmed that liposomes could effectively protect dsRNA from entering the honeybee gut and provide a reference for using RNAi technology to suppress honeybee pests and diseases.

Intestinal microbial profiles of wild Alaskan rainbow trout (Oncorhynchus mykiss) characterized by 16S rRNA amplicon data

Rainbow trout (Oncorhynchus mykiss) is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmental changes in farmed fish. In this analysis we investigated the microbiome composition of the intestinal tract in 20 wild-caught rainbow trout specimens sampled in Alaska, USA. The targeted 16S rRNA gene (V3-V4 region) was sequenced on the Illumina NovaSeq 6000 platform. After quality control, demultiplexing and adapter trimming reads were analyzed using the DADA2 pipeline to obtain Amplicon Sequencing Variants (ASVs) which were subsequently taxonomically assigned. We found two phyla dominating the gut ecosystem present in every sample, Firmicutes and Fusobacteria, followed by lower abundances of Cyanobacteria, Proteobacteria and Bacteroidetes. At the genus level, we found high relative abundances of Cetobacterium and Clostridium sensu stricto 1. Interestingly, we did not identify often dominant genera Mycoplasma, Pseudomonas or Weisella which were prevalent in numerous studies previously, in cultured rainbow trout. Wild fish are exposed to a plethora of unpredictable environmental challenges, ranging from fluctuating water temperatures to variable food availability, as opposed to controlled conditions in production facilities. Examining and comparing the gut ecosystem of wild and reared individuals holds great potential in optimizing management practices for commercially important species. Microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention and increase sustainability in aquaculture production.

VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria

This study aimed to develop a robust classification scheme for stratifying patients based on vaginal microbiome. By employing consensus clustering analysis, we identified four distinct clusters using a cohort that includes individuals diagnosed with Bacterial Vaginosis (BV) as well as control participants, each characterized by unique patterns of microbiome species abundances. Notably, the consistent distribution of these clusters was observed across multiple external cohorts, such as SRA022855, SRA051298, PRJNA208535, PRJNA797778, and PRJNA302078 obtained from public repositories, demonstrating the generalizability of our findings. We further trained an elastic net model to predict these clusters, and its performance was evaluated in various external cohorts. Moreover, we developed VIBES, a user-friendly R package that encapsulates the model for convenient implementation and enables easy predictions on new data. Remarkably, we explored the applicability of this new classification scheme in providing valuable insights into disease progression, treatment response, and potential clinical outcomes in BV patients. Specifically, we demonstrated that the combined output of VIBES and VALENCIA scores could effectively predict the response to metronidazole antibiotic treatment in BV patients. Therefore, this study's outcomes contribute to our understanding of BV heterogeneity and lay the groundwork for personalized approaches to BV management and treatment selection.

Controlling factors of iron plaque formation and its adsorption of cadmium and arsenic throughout the entire life cycle of rice plants

Iron (Fe) plaque, which forms on the surface of rice roots, plays a crucial role in immobilizing heavy metal(loids), thus reducing their accumulation in rice plants. However, the principal factors influencing Fe plaque formation and its adsorption capacity for heavy metal(loid)s throughout the rice plant's lifecycle remain poorly understood. Thus, this study investigated the dynamics of Fe plaque formation and its ability to adsorb cadmium (Cd) and arsenic (As) across different growth stages, aiming to identify the key drivers behind these processes. The findings reveal that the rate of radial oxygen loss (ROL) and the abundance of plaque-associated microbes are the primary drivers of Fe plaque formation, with their relative importance ranging from 1.4% to 81%. Similarly, the adsorption of As by Fe plaque is principally determined by the rate of ROL and the quantity of Fe plaque, with subsequent effects from the total Fe in rhizospheric soil, arsenate-reducing bacteria, and organic matter-degrading bacteria. The relative importance of these factors ranges from 6.0% to 11.7%. By contrast, the adsorption of Cd onto Fe plaque is primarily affected by competition for adsorption sites with ammonium in soils and the presence of organic matter-degrading bacteria, contributing 25.5% and 23.5% to the adsorption process, respectively. These findings provide significant insights into the development of Fe plaque and its absorption of heavy metal(loid)s throughout the lifecycle of rice plants.

Biodegradation of poly(butylene adipate terephthalate) and poly(vinyl alcohol) within aquatic pathway

Understanding the environmental fate of biodegradable plastics in aquatic systems is crucial, given the alarming amount of plastic waste and microplastic particles transported through aquatic pathways. In particular, there is a need to analyze the biodegradation of commercialized biodegradable plastics upon release from wastewater treatment plants into natural aquatic systems. This study investigates the biodegradation behaviors of poly(butylene adipate terephthalate) (PBAT) and poly(vinyl alcohol) (PVA) in wastewater, freshwater, and seawater. Biodegradation of PBAT and PVA assessed through biochemical oxygen demand (BOD) experiments and microcosm tests revealed that the type of aquatic system governs the biodegradation behaviors of each plastic, with the highest biodegradation rate achieved in wastewater for both PBAT and PVA (25.6 and 32.2 % in 30 d, respectively). Plastic release pathway from wastewater into other aquatic systems simulated by sequential incubation in different microcosms suggested that PBAT exposed to wastewater and freshwater before reaching seawater was more prone to degradation than when directly exposed to seawater. On the other hand, PVA displayed comparable biodegradation rate regardless of whether it was directly exposed to seawater or had passed through other environments beforehand. Metagenome amplicon sequencing of 16S rRNA genes revealed distinct community shifts dependent on the type of plastics in changing environments along the simulated aquatic pathway. Several bacterial species putatively implicated in the biodegradation of PBAT and PVA are discussed. Our findings underscore the significant influence of pollution routes on the biodegradation of PBAT and PVA, highlighting the potential for wastewater treatment to facilitate rapid degradation compared to direct exposure to pristine aquatic environments.

Zophobas morio versus Tenebrio molitor: Diversity in gut microbiota of larvae fed with polymers

Plastics are common synthetic materials that have been abundantly present as pollutants in natural ecosystems for the past few decades. Thus scientists have investigated the capability of plastic digestion by insects. Here we compare the effectiveness of biodegradation of the specific polymers: expanded polystyrene (EPS), polyvinyl chloride (PVC), low-density polyethylene (LDPE) and polypropylene (PP) altogether with above variants of plastics with microelements and vitamins by the mealworm - the larval form of the beetle Tenebrio molitor - and larvae of the beetle Zophobas morio, known as superworms. Z. morio beetles on all diets were able to complete their life cycle from larvae through pupae and imago, gaining 19 % and 22 % in mass on LDPE and EPS; 8 % and 7 % on PVC and PP. Mealworms (T. molitor) reared on polymers had minimal weight gain, gaining 2 % on LDPE and EPS, and a slight reduction in mass was observed when reared on PP and PVC. Not all specimens of T. molitor were able to pupate and transform to the adult stage. The results suggest that larvae of Z. morio can eat and degrade some types of plastic compounds more effectively than T. molitor. The changes in microbial gut communities were compared between these two species. The highest mass gain for Z. morio is associated with higher diversity in gut microbia and it was more diverse than that of T. molitor. Citrobacter freundii, a bacterium recognized for its ability to degrade long-chain polymers, linear hydrocarbons and cyclic hydrocarbons, was found in the microflora of Z. morio. The results confirm that superworms can survive on polymer feed. Moreover, this diet supplemented with microelements and vitamins increases the number of bacterial species and the diversity in the microbial gut.

Zoonotic potential of urban wildlife faeces, assessed through metabarcoding

Monitoring zoonoses in urban environments is of great relevance, where the incidence of certain pathogens may be higher and where population density makes the spread of any contagious disease more likely. In this study we applied a metabarcoding approach to study potentially zoonotic pathogens in faecal samples of 9 urban vertebrate species. We applied this methodology with two objectives. Firstly, to obtain information on potential pathogens present in the urban fauna of a large European city (Madrid, Spain) and to determine which are their main reservoirs. In addition, we tested for differences in the prevalence of these potential pathogens between urban and rural European rabbits, used as ubiquitous species. Additionally, based on the results obtained, we evaluated the effectiveness of metabarcoding as a tool for monitoring potential pathogen. Our results revealed the presence of potentially zoonotic bacterial genera in all studied host species, 10 of these genera with zoonotic species of mandatory monitoring in the European Union. Based on these results, urban birds (especially house sparrows and pigeons) and bats are the species posing the greatest potential risk, with Campylobacter and Listeria genera in birds and of Chlamydia and Vibrio cholerae in bats as most relevant pathogens. This information highlights the risk associated with fresh faeces from urban wildlife. In addition, we detected Campylobacter in >50 % of the urban rabbit samples, while we only detected it in 11 % of the rural rabbit samples. We found that urban rabbits have a higher prevalence of some pathogens relative to rural rabbits, which could indicate increased risk of pathogen transmission to humans. Finally, our results showed that metabarcoding can be an useful tool to quickly obtain a first screening of potentially zoonotic organisms, necessary information to target the monitoring efforts on the most relevant pathogens and host species.

Wastewater-effluent discharge and incomplete denitrification drive riverine CO2, CH4 and N2O emissions

Rivers are well-known sources of the greenhouse gasses (GHG) carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). These emissions from rivers can increase because of anthropogenic activities, such as agricultural fertilizer input or the discharge of treated wastewater, as these often contain elevated nutrient concentrations. Yet, the specific effects of wastewater effluent discharge on river GHG emissions remain poorly understood. Here, we studied two lowland rivers which both receive municipal wastewater effluent: river Linge and river Kromme Rijn. Dissolved concentrations and fluxes of CH4, N2O and CO2 were measured upstream, downstream and at discharge locations, alongside water column properties and sediment composition. Microbial communities in the sediment and water column were analysed using 16S rRNA gene sequencing. In general, observed GHG emissions from Linge and Kromme Rijn were comparable to eutrophic rivers in urban and agricultural environments. CO2 emissions peaked at most discharge locations, likely resulting from dissolved CO2 present in the effluent. CH4 emission was highest 2 km downstream, suggesting biological production by methanogenic activity stimulated by the effluents' carbon and nutrient supply. Dissolved N2O concentrations were strongly related to NO3- content of the water column which points towards incomplete riverine denitrification. Notably, methanogenic archaea were more abundant downstream of effluent discharge locations. However, overall microbial community composition remained relatively unaffected in both rivers. In conclusion, we demonstrate a clear link between wastewater effluent discharge and enhanced downstream GHG emission of two rivers. Mitigating the impact of wastewater effluent on receiving rivers will be crucial to reduce riverine GHG contributions.

Role and mechanism of Lactobacillus casei in the modulation of alcohol preference in mice

BACKGROUND

Prolonged alcohol consumption may lead to gastrointestinal tract dysfunction and cause abnormalities in the associated nervous system activity, thereby increasing the body's craving for alcohol. Lactobacillus casei is a probiotic that has been shown to reduce the incidence of alcohol-related diseases. However, it is unclear whether Lactobacillus casei can delay the development of alcohol dependence.

METHODS

The chronic intermittent active drinking method was used to establish a mouse alcohol dependence model. The mice were randomly divided into 4 treatment groups, as follows: (1) Control group: two bottles of distilled water alternately, 0.2 mL/d saline gavage. (2) Alcohol group: alternating water and alcohol, 0.2 mL/d saline gavage. (3) Low group: alternating water and alcohol, 0.2 mL/d 1 × 108CFU of Lactobacillus casei by gavage. (4) High group: alternating water and alcohol, 0.2 mL/d 1 × 109CFU of Lactobacillus casei by gavage. The daily water consumption (mL), alcohol consumption (mL) and body weight of each mouse were recorded. After that, pathological changes in the intestines, brain tissues and serum of the experimental animals were detected, while changes in the intestinal flora of the mice were analysed by 16S rRNA sequencing.

RESULTS

The Lactobacillus casei intervention did not produce a significant effect on body weight in alcohol-exposed mice (P>0.05), but significantly reduced alcohol preference in alcohol-exposed mice (P<0.05). Subsequent analyses showed that Lactobacillus casei significantly ameliorated intestinal, brain tissue, and systemic inflammatory responses in alcohol-exposed mice (P<0.05). 16S rRNA sequencing showed that alcohol-exposed mice treated with Lactobacillus casei exhibited a richer composition of intestinal microorganisms, such as f__Rikenellaceae, g__Alistipes_A_871400, and g__Bacteroides_H genera showed relative enrichment in the High group.

CONCLUSION

By showing that Lactobacillus casei slows down alcohol preference and alleviates gut and brain tissue inflammation in alcohol-exposed mice, our findings provide a possible strategy: Lactobacillus casei may be able to serve as a potential target for the prevention and treatment of alcohol dependence.

Mechanisms of N-doped microporous biochar decreased Cd transition in rhizosphere soils and its impact on soil bacterial community composition

Soil cadmium (Cd) contamination has garnered considerable attention. This study employed batch sorption experiments and rhizobox experiments to examine the impact of nitrogen-doped microporous biochar (NBB) on the temporal and spatial distribution of Cd in the rhizosphere of rice plants, with the aim of elucidating the underlying mechanisms. The results indicated that the adsorption of Cd(II) onto NBB was predominantly governed by chemical reactions. When applied to soil, the NBB significantly hindered the migration of Cd from the bulk soil to the rhizosphere. Additionally, the application of NBB decreased the redox potential (Eh) in the rhizosphere soil and increased the relative abundance of Anaeromyxobacteraceae, Geobacteraceae, Desulfurisporaceae, and Syntrophomonadaceae, which could facilitate the reduction of soil Cd availability. Furthermore, the NBB2 treatment encouraged the formation of iron plaque on the root surface, thereby limiting the uptake of Cd from the soil into the root system. Moreover, the N-doped microporous biochar treatment resulted in lower Cd levels in the stele of root, an effect that was associated with increased sulfur (S) content in the stele and epidermis, suggesting a potential role for S in Cd sequestration. Ultimately, the application of N-doped microporous biochar resulted in diminished Cd accumulation in the rice tissues.

Cascading sulfur cycling in simulated oil sands pit lake water cap mesocosms transitioning from oxic to euxinic conditions

Base Mine Lake (BML), the first full-scale demonstration of oil sands tailings pit lake reclamation technology, is experiencing expansive, episodic hypolimnetic euxinia resulting in greater sulfur biogeochemical cycling within the water cap. Here, Fluid Fine Tailings (FFT)-water mesocosm experiments simulating the in situ BML summer hypolimnetic oxic-euxinic transition determined sulfur biogeochemical processes and their controlling factors. While mesocosm water caps without FFT amendments experienced limited geochemical and microbial changes during the experimental period, FFT-amended mesocosm water caps evidenced three successive stages of S speciation in ∼30 days: (S1) rising expansion of water cap euxinia from FFT to water surface; enabling (S2) rapid sulfate (SO42-) reduction and sulfide production directly within the water column; fostering (S3) generation and subsequent consumption of sulfur oxidation intermediate compounds (SOI). Identified key SOI, elemental S and thiosulfate, support subsequent SOI oxidation, reduction, and/or disproportionation processes in the system. Dominant water cap microbes shifted from methanotrophs and denitrifying/iron-reducing bacteria to functionally versatile sulfur-reducing bacteria (SRB) comprising sulfate-reducing bacteria (Desulfovibrionales) and SOI-reducing/disproportionating bacteria (Campylobacterales and Desulfobulbales). The observed microbial shift is driven by decreasing [SO42-] and organic aromaticity, with putative hydrocarbon-degrading bacteria providing electron donors for SRB. Comparison between unsterile and sterile water treatments further underscores the biogeochemical readiness of the in situ water cap to enhance oxidant depletion, euxinia expansion and establishment of water cap SRB communities aided by FFT migration of anaerobes. Results here identify the collective influence of FFT and water cap microbial communities on water cap euxinia expansion associated with sequential S reactions that are controlled by concentrations of oxidants, labile organic substrates and S species. This emphasizes the necessity of understanding this complex S cycling in assessing BML water cap O2 persistence.

The impact of anthropogenic pressures on microbial diversity and river multifunctionality relationships on a global scale

Conserving biodiversity is crucial for maintaining essential ecosystem functions, as indicated by the positive relationships between biodiversity and ecosystem functioning. However, the impacts of declining biodiversity on ecosystem functions in response to mounting human pressures remain uncertain. This uncertainty arises from the complexity of trade-offs among human activities, climate change, river properties, and biodiversity, which have not been comprehensively addressed collectively. Here, we provide evidence that river biodiversity was significantly and positively associated with multifunctionality and contributed to key ecosystem functions such as microbially driven water purification, leaf litter decomposition and pathogen control. However, human pressure led to abrupt changes in microbial diversity and river multifunctionality relationships at a human pressure value of 0.5. In approximately 30 % (N = 58) of countries globally, the ratio of area above this threshold exceeded the global average (∼11 %), especially in Europe. Results show that human pressure affected ecosystem functions through direct effects and interactive effects. We provide more direct evidence that the nonadditive effects triggered by prevailing human pressure impact the multifunctionality of rivers globally. Under high levels of human stress, the beneficial effects of biodiversity on nutrient cycling, carbon storage, gross primary productivity, leaf litter decomposition, and pathogen control tend to diminish. Our findings highlight that considering interactions between human pressure and local abiotic and biotic factors is key for understanding the fate of river ecosystems under climate change and increasing human pressure.

Longitudinal bacterial community dynamics and sodium hypochlorite intervention in a newly built university building

Urbanisation and building advancements have increased microbial growth in indoor environments, altering human interactions with these microorganisms. Restrooms and their sinks harbour diverse bacterial communities, that differ from those found in natural environments, that could have negative implications for human health. Over two and a half years, this study examined the diversity, temporal dynamics, and resilience of bacterial communities in restroom sink P-traps in a newly built university building. Structured into two phases, the first phase consisted of continuous monitoring of bacterial community dynamics for two years (n = 352), while the second phase involved an intervention with sodium hypochlorite (bleach) and subsequent sampling (n = 132). In the first phase, we show that sink communities converge, becoming more compositionally similar to other sinks within the building. Bacterial families such as Rhodocyclaceae and Flavobacteriaceae dominated across the sinks, and others such as Comamonadaceae, Moraxellaceae and Enterbacteriaceae were highly prevalent. When comparing bacterial structure and composition to other sinks located on the university campus, the mean bacterial dissimilarity decreased over time, indicating compositional similarity, particularly with the newer buildings on campus. The second phase demonstrated resilience by the bacterial sink communities. Following bleach treatments, a distinct increase in Acinetobacter was observed. However, by the fourth week after bleach invention, bacterial communities had re-established to levels observed prior to treatment. This study had the unique opportunity to sample a newly built building before occupancy and for the subsequent two and a half years. The findings provide crucial insights into the development and resilience of sink P-trap bacterial communities in restrooms, laying the groundwork for more targeted approaches to disinfection strategies.

Long term impact of electrical resistance heating on soil bacterial community based on a field test

Thermal remediation is an effective technology for organic contaminant remediation. However, the application of thermal remediation may have negative effects on soil properties and ecological functions, which requires further investigation. Based on a pilot test of electrical resistance heating remediation (ERH), soil samples were collected at different locations after heating for 116 days. Most soil physicochemical properties were less affected by the heating temperature difference. Application of high temperature increased microbial abundance but inhibited alpha diversity of the bacterial community. More significant changes in microbial communities were observed at temperatures above 60 °C. The genera mainly affected by heating temperature included Flavobacteria, Brockia, and S085, while the increase in temperature also inhibited the abundance of nitrochlorobenzene functional genes. At 140 days after the end of the pilot test, the bacterial community affected by thermal remediation could recover effectively, and the recovery of the bacterial community was not affected by temperature difference during the heating period. This study provides valuable field evidence of the long term impact of soil ERH treatment on soil properties and microbial communities, and provides further references for optimization of remediation performance with coupled technologies.

Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest

The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.

Exposure pattern of triclosan and tetracycline change their impacts on methanogenic digestion microbiomes

Triclosan (TCS) and tetracycline (TC) as common antibacterial agents are frequently detected in the influent of wastewater treatment plants. The TCS and TC exposure patterns may determine their impacts on wastewater treatment microbiomes, on which information remains unknown. In this study, the impacts of sequential exposure of TCS and TC on methanogenic digestion microbiomes in upflow anaerobic sludge blanket (UASB) reactors were analyzed and compared with that of the same microbiomes being simultaneously exposed to TCS and TC. Results indicated that the UASB reactor 2 (MD2) with sequential TCS-TC exposure consistently demonstrated higher chemical oxygen demand (COD) removal efficiency (94.7 %). In contrast, in the MD1 reactor, COD removal efficiency decreased from 94.4 % to 82.7 % upon simultaneous exposure to TCS and TC. Accordingly, a 1.8 times higher enrichment of total antibiotic resistance genes (ARGs) was observed in MD1 relative to MD2. Using a dissimilarity-overlap approach, the MD2 microbiome with sequential exposure was predominantly mediated by deterministic factors in their community assembly (largely contributed by abundant and intermediate biospheres), resulting in microbial interaction networks with higher average clustering coefficients and shorter average path lengths, compared to the MD1 microbiomes. Our results could support sustainable management of TCS and TC contamination in wastewater treatment plants.

Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils

Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.

Significant correlations between heavy metals and prokaryotes in the Okinawa Trough hydrothermal sediments

Prokaryotes play crucial roles in hydrothermal vent ecosystems, yet their interactions with heavy metals are not well understood. This study explored the diversity of prokaryotic communities and their correlations with heavy metals and nutrient elements in hydrothermal sediments from Okinawa Trough. A total of 117 bacterial genera in 26 bacterial phyla and 10 archaeal classes in 3 archaeal phyla were identified, including dominant prokaryotic phyla Planctomycetes, Acidobacteria, Verrucomicrobia, and Euryarchaeota. Furthermore, Fe (39.61 mg/g), Mn (2.84 mg/g) and Ba (0.36 mg/g) were found to be the most abundant heavy metals in the Okinawa hydrothermal sediments. Notably, the concentrations of Zn, Ba, Mn, total organic carbon, and total nitrogen significantly increased, whereas the total sulfur concentration distinctively decreased at sampling sites farther from hydrothermal vents. These changes corresponded with reductions in prokaryotic abundance and diversity. Most heavy metals, including Mn, Fe, Co, Cu and As, presented significant positive correlations with a number of prokaryotic genera in the nearby sediment samples. In contrast, both positive and negative correlations with prokaryotes were observed in remote sediment. The keystone taxa include Magnetospirillum, GOUTA19, Lysobacter, Kaistobacter, Treponema, and Clostridium were detected through prokaryote interspecies interactions. The functional predictions revealed significant genes involved in carbon fixation, nitrogen/sulfur cycling, heat shock protein, and metal resistance pathways. Structural equation modeling confirmed that metal and nutrient elements directly influence the composition of prokaryotic communities, which in turn affects the relative abundance of functional genes.

Efficient elimination of antibiotics and antibiotic resistance genes in hyperthermophilic sludge composting

Composting is widely applied in recycling ever-increasing sewage sludge. However, the insufficient elimination of antibiotics and antibiotic resistance genes (ARGs) in conventional compost fertilizer poses considerable threat to agriculture safety and human health. Here we investigated the efficacy and potential mechanisms in the removal of antibiotics and ARGs from sludge in hyperthermophilic composting (HTC) plant. Our results demonstrated that the HTC product was of high maturity. HTC led to complete elimination of antibiotics and potential pathogens, as well as removal of 98.8 % of ARGs and 88.1 % of mobile genetic elements (MGEs). The enrichment of antibiotic-degrading candidates and related metabolic functions during HTC suggested that biodegradation played a crucial role in antibiotic removal. Redundancy analysis (RDA) and structural equation modelling (SEM) revealed that the reduction of ARGs was attributed to the decline of ARG-associated bacteria, mainly due to the high-temperature selection. These findings highlight the feasibility of HTC in sludge recycling and provide a deeper understanding of its mechanism in simultaneous removal of antibiotics and ARGs.

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16-0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41-69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from "nitrification-denitrification" in the recharge area to "partial nitrification-anammox" in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

The impact of long-term (≥5 years) cholecystectomy on gut microbiota changes and its influence on colorectal cancer risk: based on 16S rDNA sequencing analysis

BACKGROUND

Colorectal cancer (CRC) continues to be a major global health concern. Recent advances in molecular biology have highlighted the gut microbiota's role in CRC. This study investigates long-term (≥5 years) gut microbiota changes in patients postcholecystectomy, comparing them with CRC patients and healthy controls to assess their impact on CRC development.

METHODS

Sixty participants were divided into three groups: 20 healthy controls, 20 postcholecystectomy (PCE) patients, and 20 CRC patients. Demographic data and stool samples were collected. Gut microbiota composition, abundance, and diversity were analyzed using high-throughput 16S rDNA sequencing.

RESULTS

Significant differences in microbial community, α-diversity ( P  < 0.05) and β-diversity ( P  = 0.006), were observed among the three groups. At the phylum level, Firmicutes abundance was significantly reduced in PCE and CRC groups compared with the control group ( P  = 0.002), while changes in other phyla were not significant ( P >0.05). At the genus level, Bacteroides , Dialister , and Parabacteroides increased progressively from control to PCE to CRC groups ( P  = 0.004, 0.001, and 0.002). Prevotella decreased across these groups ( P  = 0.041). Faecalibacterium and Roseburia abundances were reduced in PCE and CRC groups compared with controls ( P  = 0.001 and 0.003). The Random Forest algorithm identified Parabacteroides , Bacteroides , Roseburia , and Dialister as key distinguishing genera.

CONCLUSION

The gut microbiota of long-term (≥5 years) PCE patients significantly differs from that of controls and resembles that of CRC patients, suggesting a potential link between cholecystectomy and CRC development through key microbial changes.

Distinct metabolites affect the phloem fungal communities in ash trees (Fraxinus spp.) native and nonnative to the highly invasive emerald ash borer (AGRILUS PLANIPENNIS)

Emerald ash borer (EAB, Agrilus planipennis) is an invasive killer of ash trees (Fraxinus spp.) in North America and Europe. Ash species co-evolved with EAB in their native range in Asia are mostly resistant, although the precise mechanism(s) remain unclear. Very little is also known about EAB or ash tree microbiomes. We performed the first joint comparison of phloem mycobiome and metabolites between a native and a nonnative ash species, infested and uninfested with EAB, in conjunction with investigation of larval mycobiome. Phloem mycobiome communities differed between the tree species, but both were unaffected by EAB infestation. Several indicator taxa in the larval gut shared a similarly high relative abundance only with the native host trees. Widely targeted metabolomics revealed 24 distinct metabolites in native trees and 53 metabolites in nonnative trees, respectively, that differed in relative content between infested and uninfested trees only in one species. Interestingly, four metabolites shared a strong relationship with the phloem mycobiomes, majority of which affected only the native trees. Collectively, our results demonstrate a complex interplay between host tree chemistry and mycobiome, and suggest the shared relationships between the mycobiomes of the native host tree and EAB may reflect their shared co-evolution.

Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition

The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.

The effect of peanut skins as a natural antimicrobial feed additive on ileal and cecal microbiota in broiler chickens inoculated with Salmonella enterica Enteritidis

The consumption of poultry products contaminated with Salmonella species is one of the most common causes of Salmonella infections. In vivo studies demonstrated the potential application of peanut skins (PS) as an antimicrobial poultry feed additive to help mitigate the proliferation of Salmonella in poultry environments. Tons of PS, a waste by-product of the peanut industry, are generated and disposed in U.S. landfills annually. Peanut skins and extracts have been shown to possess antimicrobial and antioxidant properties. Hence, we aimed to determine the effect of PS as a feed additive on the gut microbiota of broilers fed a control or PS supplemented (4% inclusion) diet and inoculated with or without Salmonella enterica Enteritidis (SE). At hatch 160 male broilers were randomly assigned to 4 treatments: 1) CON-control diet without SE, 2) PS-PS diet without SE, 3) CONSE-control diet with SE, 4) PSSE-PS diet with SE. On d 3, birds from CONSE and PSSE treatments were inoculated with 4.2 × 109 CFU/mL SE. At termination (4 wk), 10 birds/treatment were euthanized and ileal and cecal contents were collected for 16S rRNA analysis using standard methodologies. Sequencing data were analyzed using QIIME2. No effect of PS or SE was observed on ileal alpha and beta diversity, while evenness, richness, number of amplicon sequence variants (ASV) and Shannon, as well as beta diversity were significantly (P < 0.05) affected in ceca. Similarly, more differentially abundant taxa between treatment groups were identified in ceca than in ileum. However, more microbiota functional changes, based on the PICRUST2 prediction, were observed in ileum. Overall, relatively minor changes in microbiota were observed during SE infection and PS treatment, suggesting that PS addition may not attenuate the SE proliferation, as shown previously, through modulation of microbiota in gastrointestinal tract. However, while further studies are warranted, these results suggest that PS may potentially serve as a functional feed additive for poultry for improvement of animal health.

Native and non-native freshwater bivalves in the bioremediation of bacterial pollution caused by the disposal of sewage

Treated sewage contains a large diversity of pathogens that can be transmitted to the environment and, directly or indirectly, infect humans through water use (i.e., consumption, bathing, or irrigation). In urban environments, wastewater normally flows into wastewater treatment plants (WWTPs), where it is subjected to different processes in order to eliminate the greatest amount of waste. However, there are inequalities among European countries concerning wastewater management. In this context, we evaluate the potential of freshwater mussels to improve water quality (i.e., reduce bacterial abundance) in rivers receiving primary, secondary, or tertiary sewage-treated effluents. Additionally, because freshwater mussels are declining at a global scale and empty niches are progressively occupied by non-native counterparts, we evaluate if depauperate communities and the Asian clams, Corbicula genus, can provide equivalent ecosystem services (i.e., water quality improvement by biofiltration) formerly provided by diverse native communities. For this, an analysis of the bacterial biodiversity of the samples filtered by the different bivalve communities was carried out. The experimental approach was performed by metabarcoding the 16S rRNA gene using Illumina technologies. According to the results obtained, secondary treatment processes were effective in reducing the bacterial diversity. Furthermore, the waters filtered by the bivalves presented a lower bacterial abundance for certain genera. Biofiltration differs, however, among species, with Corbicula reducing a large number of taxa much more efficiently than native freshwater mussels in both diverse and depauperated communities. These results are likely related to Corbicula being a generalist species in front of native mussels, which may be more selective. Considering it is not possible to eradicate Corbicula from European rivers, its filtering capacity should be considered when managing freshwater ecosystems.

Refractory wastewater shapes bacterial assembly and key taxa during long-term acclimatization

Bacterial assembly and key taxa during long-term acclimatization in refractory wastewater treatment systems is of paramount importance for optimizing system performance and improving management strategies. Therefore, this study employed high-throughput sequencing, coupled with machine learning models and statistical analysis approaches, to comprehensively elucidate key features of bacterial communities and assembly processes in pesticide wastewater treatment systems. A nine-month monitoring showed substantial variation in diversity and composition of bacterial community between two interconnected biological treatment units (designated as BA and PA). Dynamics of bacterial communities in both units were similar. Moreover, water quality played crucial roles in regulating the bacterial community structure of activated sludge, which were primarily driven by deterministic patterns. Homogeneous selection contributed to 62.85 % and 64.43 % of the variations in BA and PA samples, respectively. Additionally, network analysis revealed significant modularity in bacterial compositions in both groups. Linear regression analysis identified major bacterial modules associated with metabolism and degradation functions. Notably, Module 2 in PA samples has significant positive correlations with functions related to metabolism of nucleotide, amino acid, and xenobiotics, as well as benzoate degradation. Furthermore, key taxa in ecological modules identified by Random Forest model, such as Pseudomonas, Sphingobium, and PHOS-HE28, were dominant populations with metabolism and degradation functions. Particularly, Sphingobium, appeared to be a potential multifunctional degrading bacterium, related to amino acid and xenobiotics metabolism, as well as fatty acid, valine, leucine, isoleucine, fluorobenzoate, and aminobenzoate degradation. These findings are important for developing operating strategies to maintain stable system performance during refractory wastewater treatment.

Characteristics of the oral microbiome in youth exposed to caregiving adversity

Caregiving adversity (CA) exposure is robustly linked to increased risk for poor oral, physical, and mental health outcomes. Increasingly, the gut microbiome has garnered interest as a contributor to risk for and resilience to such health outcomes in CA-exposed individuals. Though often overlooked, the oral microbiome of CA-exposed individuals may be just as important a contributor to health outcomes as the gut microbiome. Indeed, outside the context of CA, the oral microbiome is well-documented as a regulator of both oral and systemic health, and preliminary data suggest its association with mental health. However, research examining the association between CA and the oral microbiome is extremely sparse, especially in childhood, when the community composition of such organisms is still stabilizing. To address that sparsity, in the current study, we examined composition and differential abundance metrics of the oral microbiome in 152 youth aged 6-16 years, who had either been exposed to significant caregiving adversity (significant separation from or maltreatment by a caregiver; N = 66, CA) or who had always remained with their biological/birth families (N = 86, Comparison). We identified a significant negative association between hair cortisol and oral microbiome richness in the Comparison group that was significantly blunted in the CA group. Additionally, youth in the CA group had altered oral microbiome composition and elevated abundance of potentially pathogenic bacteria relative to youth in the Comparison group. Questionnaire measures of fatigue, somatic complaints, and internalizing symptoms had limited associations with oral microbiome features that were altered in CA. Although we found differences in the oral microbiomes of CA-exposed youth, further research is required to elucidate the implications of those differences for health and well-being.

Using machine learning to identify environmental factors that collectively determine microbial community structure of activated sludge

Activated sludge (AS) microbial communities are influenced by various environmental variables. However, a comprehensive analysis of how these variables jointly and nonlinearly shape the AS microbial community remains challenging. In this study, we employed advanced machine learning techniques to elucidate the collective effects of environmental variables on the structure and function of AS microbial communities. Applying Dirichlet multinomial mixtures analysis to 311 global AS samples, we identified four distinct microbial community types (AS-types), each characterized by unique microbial compositions and metabolic profiles. We used 14 classical linear and nonlinear machine learning methods to select a baseline model. The extremely randomized trees demonstrated optimal performance in learning the relationship between environmental factors and AS types (with an accuracy of 71.43%). Feature selection identified critical environmental factors and their importance rankings, including latitude (Lat), longitude (Long), precipitation during sampling (Precip), solids retention time (SRT), effluent total nitrogen (Effluent TN), average temperature during sampling month (Avg Temp), mixed liquor temperature (Mixed Temp), influent biochemical oxygen demand (Influent BOD), and annual precipitation (Annual Precip). Significantly, Lat, Long, Precip, Avg Temp, and Annual Precip, influenced metabolic variations among AS types. These findings emphasize the pivotal role of environmental variables in shaping microbial community structures and enhancing metabolic pathways within activated sludge. Our study encourages the application of machine learning techniques to design artificial activated sludge microbial communities for specific environmental purposes.