Improved bacterial composition and co-occurrence patterns of rhizosphere increased nutrient uptake and grain yield through cultivars mixtures in maize

Crop diversification contributes to agricultural productivity and resources efficient utilization. However, whether cultivar mixtures in maize affects soil bacterial community, nutrient uptake, plant growth and yield remains unknown. A two-year lysimetric experiment was conducted using two maize cultivars (LY16 and JS501) with different root system architectures planted in monoculture or in mixture under normal fertilization (NF), reduced fertilization (RF) or no addition of fertilizer (CK) and was assessed at the silking stages. Cultivar mixtures and monoculture of LY16 had higher shoot biomass, nutrient uptake and total root length at silking stage, and grain yield than monoculture of JS501 under NF and RF conditions. Under NF and RF conditions, cultivar mixtures and monoculture of LY16 led to an increase in bacterial diversity, significant changes in community structure, and a high abundance of Bacteroidia and biomarkers of Chitinophagaceae and Saprospiraceae (Bacteroidia). Cultivar mixtures showed specific responses from modules of the rhizosphere bacterial community co-occurrence network, and the relative abundance of keystone taxa of cultivar mixtures was higher than that of monoculture of JS501. The keystone taxa had a broad and significant positive correlation with plant nutrient accumulation and grain yield. Cultivar mixtures showed similar assembly processes of Bacteroidia with monoculture of LY16, and the increased abundance of Chitinophagaceae may lead to a healthy rhizosphere bacterial community. Overall, our findings indicate that cultivar mixtures significantly affects the assembly and composition of the rhizosphere bacterial community, and thus benefits plant nutrient acquisition and plant growth. These findings could deepen our understanding of the facilitating effect of rhizosphere functional microbial community (e.g. plant nutrition uptake or immunity)of cultivar mixtures.

Antihyperalgesic properties of gut microbiota: Parabacteroides distasonis as a new probiotic strategy to alleviate chronic abdominal pain

ABSTRACT

The potential role of gut microbiota in pain modulation is arousing an emerging interest since recent years. This study investigated neuromodulatory properties of gut microbiota to identify next-generation probiotics to propose alternative therapies for visceral pain management. Neuromodulation ability of 10 bacterial strains isolated from a healthy donor was assessed both on ND7/23 immortalized cell line and primary neuronal cells from rat dorsal root ganglia. This screening highlighted the neuroinhibitory property of Parabacteroides distasonis (F1-2) strain, supported both by its intracellular content and membrane fraction, which was further investigated in visceral pain mouse models. Oral administration of F1-2 resulted in a significant decrease of colonic hypersensitivity (CHS) in dextran sulfate sodium (0.5%) model associated with low-grade inflammation and a significant decrease of CHS in Citrobacter rodentium postinfectious models. No effect of F1-2 oral administration on CHS was observed in a neonatal maternal separation stress model. Antihyperalgesic effect unlikely involved modulation of inflammatory processes or restoration of intestinal barrier. Exploration of direct dialogue mechanisms between this strain and nervous system, assessed by calcium imaging experiments, revealed that F1-2 interacts directly with nociceptors by reducing activation level on capsaicin, inflammatory soup, and bradykinin stimulations. Our study provides new insights about bacteria-host interaction and places P distasonis as a potential therapeutic strategy in the treatment of visceral pain observed in leaky gut-associated pathologies.

An in-depth investigation of the microbiota and its virulence factors associated with severe udder cleft dermatitis lesions

Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the microbiota in severe UCD lesions versus healthy udder skin by putting forward a taxonomic and functional profile based on a virulence factor analysis. Through shotgun metagenomic sequencing, we found a high proportion of bacteria in addition to a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares analysis on the metagenomic data. Proteobacteria, Bacillota, and Actinomycetota were among the most abundant phyla in healthy udder skin samples. In UCD samples, Bacteroidota was the most abundant phylum. At genus level, Bifidobacterium spp. had the highest relative abundance in healthy skin samples, whereas Porphyromonas spp. and Corynebacterium spp. had the highest relative abundance in UCD samples. In the differential abundance analysis, Porphyromonas spp. and Bacteroides spp. were significantly differentially abundant in UCD samples, whereas Bifidobacterium spp., Staphylococcus sp. AntiMn-1, and Staphylococcus equorum were more commonly found in healthy samples. Moreover, the abundance of several treponeme phylotypes was significantly higher in lesion samples. The streptococcal cysteine protease speB was among the most abundant virulence factors present in severe UCD lesions, while a plethora of virulence factors such as the antitoxin relB were downregulated, possibly contributing to creating the ideal wound climate for the dysbiotic community. Network analysis showed healthy lesion samples had a large network ofpositive, correlations between the abundances of beneficial species such as Aerococcus urinaeequi and Bifidobacterium angulatum, indicating that the healthy skin microbiome forms an active protective bacterial network, which is disrupted in case of UCD. In UCD samples, a smaller microbial network mainly consisting of positive correlations between the abundances of Bacteroides fragilis and anaerobic Bacteroidota was exposed. Moreover, a high correlation between the taxonomic data and virulence factors was revealed, concurrently with 2 separate networks of microbes and virulence factors. One network, matching with the taxonomic findings in the healthy udder skin samples, showcased a community of harmless or beneficial bacteria, such as Bifidobacterium spp. and Butyrivibrio proteoclasticus, associated with hcnB, hcnC, relB, glyoxalase, and cupin 2. The other network, corresponding to UCD samples, consisted of pathogenic or facultative pathogenic and mainly anaerobic bacteria such as Treponema spp., Mycoplasmopsis spp., and bovine gammaherpesvirus 4, that correlated with virulence factors SpvB, fhaB, and haemagglutination activity domain-associated factor. Our results point toward a dysbiotic community with a notable decrease in diversity and evenness, with a loss of normal skin inhabitants and innocuous or useful species making way for predominantly anaerobic, facultative pathogens. The shift in the abundance of virulence factors such as fhaB and SpvB could play a role in the manifestation of a local micro-environment favorable to the microbiome associated with udder skin lesions. Lastly, the presence of specific networks between microbial species, and between microbes and virulence factors was shown.

Sciadonic acid ameliorates cyclophosphamide-induced immunosuppression by modulating the immune response and altering the gut microbiota

BACKGROUND

Cyclophosphamide (Cy) is a frequently used chemotherapeutic drug, but long-term Cy treatment can cause immunosuppression and intestinal mucosal damage. The intestinal mucosal barrier and gut flora play important roles in regulating host metabolism, maintaining physiological functions and protecting immune homeostasis. Dysbiosis of the intestinal flora affects the development of the intestinal microenvironment, as well as the development of various external systemic diseases and metabolic syndrome.

RESULTS

The present study investigated the influence of sciadonic acid (SA) on Cy-induced immunosuppression in mice. The results showed that SA gavage significantly alleviated Cy-induced immune damage by improving the immune system organ index, immune response and oxidative stress. Moreover, SA restored intestinal morphology, improved villus integrity and activated the nuclear factor κB signaling pathway, stimulated cytokine production, and reduced serum lipopolysaccharide (LPS) levels. Furthermore, gut microbiota analysis indicated that SA increased t beneficial bacteria (Alistipes, Lachnospiraceae_NK4A136_group, Rikenella and Odoribacter) and decreased pathogenic bacteria (norank-f-Oscillospiraceae, Ruminococcus and Desulfovibrio) to maintain intestinal homeostasis.

CONCLUSION

The present study provided new insights into the SA regulation of intestinal flora to enhance immune responses. © 2024 Society of Chemical Industry.

Effects of chronic unpredictable mild stress on gut microbiota and fecal amino acid and short-chain fatty acid pathways in mice

Depression is a serious disease that has a significant impact on social functioning. However, the exact causes of depression are still not fully understood. Therefore, it is necessary to explore new pathways leading to depression. In this study, we used 16 S rDNA to examine changes in gut microbiota and predict related pathways in depression-like mice. Additionally, we employed liquid chromatography-mass spectrometry (LC-MS) to identify changes in amino acids and gas chromatography-mass spectrometry (GC-MS) to identify changes in short-chain fatty acids (SCFAs) in fecal samples. We conducted Pearson/Spearman correlation analysis to investigate the associations between changes in amino acids/SCFAs and behavioral outcomes. The 16 S rDNA sequencing revealed significant alterations in gut microbiota at the phylum and genus levels in mice subjected to chronic unpredictable mild stress (CUMS). The relative abundances of Bacteroidetes, Proteobacteria, Bacteroides, and Alloprevotella were increased, while Firmicutes, Verrucomicrobia, Actinobacteria, Lactobacillus, Akkermansia, Lachnospirillum, and Enterobacter were decreased in the CUMS mice. We used PICRUSt software to annotate the kyoto encyclopedia of genes and genomes (KEGG) pathway function related to depression-like behavior in mice. Our analysis identified sixty functional pathways associated with the gut microbiota of mice exhibiting depression-like behavior. In the amino acid concentration analysis, we observed decreased levels of hydroxyproline and tryptophan, and increased levels of alanine in CUMS mice. In the SCFAs concentration assay, we found decreased levels of butyric acid and valeric acid, and increased levels of acetic acid in CUMS mice. Some of these changes were significantly correlated with depressive-like behaviors. Our study contributes to the understanding of the mechanism of the gut-brain axis in the occurrence and development of depression.

Improved microalgae growth and lipid production in anaerobic digestate with ultraviolet radiation pretreatment

Inappropriate sterilization strategies inhibit microalgal growth when culturing microalgae with anaerobic digestate. This study aimed to scientifically select a low-cost disinfection pretreatment of anaerobic digestate for large-scale microalgae cultivations. In this work, three different methods, including autoclaving, ultraviolet or NaClO treatments, were employed to sterilize the municipal anaerobic digestate. Scenedesmus quadricauda was then cultured in diluted liquid digestate for the simultaneous lipid production and nutrient removal. The results indicated that the growth of S. quadricauda was inhibited after NaClO treatment due to the residual free chlorine. The 15-min ultraviolet effectively mitigated microbial contamination and increasing nutrient availability, enhancing the electron transport of microalgal photosynthesis. After 6-days cultivation, the microalgal biomass concentration of the ultraviolet group was 1.09 g/L, comparable to that of the autoclaving group (1.15 g/L). High nutrient removal efficiency was observed: COD (93.30 %), NH4+-N (92.56 %), TN (85.82 %) and TP (95.12 %). Moreover, S. quadricauda outcompeted the indigenous microorganisms, contributing to its dominance in the culture system of ultraviolet group. The facultative anaerobe Comamonadaceae and aerobes Moraxellaceae, rather than strict anaerobe Paludibacteraceae and Bacteroidetes_vadinHA17, played vital roles in synergistic removal of contaminants by bacteria and algae. The potential competition for nitrogen and phosphorus by bacteria contributed to the ultraviolet group having the greatest lipid content (48.19 %). Therefore, this work suggested using 15-min ultraviolet treatment for anaerobic digestate in large-scale microalgae cultivation.

Structural characteristics of gut microbiota in longevity from Changshou town, Hubei, China

The gut microbiota (GM) and its potential functions play a crucial role in maintaining host health and longevity. The aim of this study was to investigate the potential relationship between GM and longevity. We collected fecal samples from 92 healthy volunteers (middle-aged and elderly: 43-79 years old; longevity: ≥ 90 years old) from Changshou Town, Zhongxiang City, Hubei, China. In addition, we collected samples from 30 healthy middle-aged and elderly controls (aged 51-70 years) from Wuhan, Hubei. The 16S rDNA V3 + V4 region of the fecal samples was sequenced using high-throughput sequencing technology. Diversity analysis results showed that the elderly group with longevity and the elderly group with low body mass index (BMI) exhibited higher α diversity. However, no significant difference was observed in β diversity. The results of the microbiome composition indicate that Firmicutes, Proteobacteria, and Bacteroidota are the core phyla in all groups. Compared to younger elderly individuals, Akkermansia and Lactobacillus are significantly enriched in the long-lived elderly group, while Megamonas is significantly reduced. In addition, a high abundance of Akkermansia is a significant characteristic of elderly populations with low BMI values. Furthermore, the functional prediction results showed that the elderly longevity group had higher abilities in short-chain fatty acid metabolism, amino acid metabolism, and xenobiotic biodegradation. Taken together, our study provides characteristic information on GM in the long-lived elderly population in Changshou Town. This study can serve as a valuable addition to the current research on age-related GM. KEY POINTS: • The gut microbiota of elderly individuals with longevity and low BMI exhibit higher alpha diversity • Gut microbiota diversity did not differ significantly between genders in the elderly population • Several potentially beneficial bacteria (e.g., Akkermansia and Lactobacillus) are enriched in long-lived individuals.

Microbial community structure and diversity attached to the periphyton in different urban aquatic habitats

Periphyton is a complex community composed of diverse prokaryotes and eukaryotes; understanding the characteristics of microbial communities within periphyton becomes crucial for biogeochemical cycles and energy dynamics of aquatic ecosystems. To further elucidate the community characteristics of periphyton across varied aquatic habitats, including unpolluted ecologically restored lakes, aquaculture ponds, and areas adjacent to domestic and industrial wastewater treatment plant outfalls, we explored the composition and diversity of prokaryotic and eukaryotic communities in periphyton by employing Illumina MiSeq sequencing. Our findings indicated that the prokaryotic communities were predominantly composed of Proteobacteria (40.92%), Bacteroidota (21.01%), and Cyanobacteria (10.12%), whereas the eukaryotic communities were primarily characterized by the dominance of Bacillariophyta (24.09%), Chlorophyta (20.83%), and Annelida (15.31%). Notably, Flavobacterium emerged as a widely distributed genus among the prokaryotic community. Unclassified_Tobrilidae exhibited higher abundance in unpolluted ecologically restored lakes. Chaetogaster and Nais were enriched in aquaculture ponds and domestic wastewater treatment plant outfall area, respectively, while Surirella and Gomphonema dominated industrial sewage treatment plant outfall area. The alpha diversity of eukaryotes was higher in unpolluted ecologically restored lakes. pH and nitrogen content (NO 2 - - N ,NO 3 - - N , and TN) significantly explained the variations for prokaryotic and eukaryotic community structures, respectively. Eukaryotic communities exhibited a more pronounced response to habitat variations compared to prokaryotic communities. Moreover, the association networks revealed an intensive positive correlation between dominant Bacillariophyta and Bacteroidota. This study provided useful data for identifying keystone species and understanding their ecological functions.

Akkermansia muciniphila and Parabacteroides distasonis synergistically protect from colitis by promoting ILC3 in the gut

Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the gastrointestinal tract. The etiology of IBD remains elusive, but the disease is suggested to arise from the interaction of environmental and genetic factors that trigger inadequate immune responses and inflammation in the intestine. The gut microbiome majorly contributes to disease as an environmental variable, and although some causative bacteria are identified, little is known about which specific members of the microbiome aid in the intestinal epithelial barrier function to protect from disease. While chemically inducing colitis in mice from two distinct animal facilities, we serendipitously found that mice in one facility showed remarkable resistance to disease development, which was associated with increased markers of epithelial barrier integrity. Importantly, we show that Akkermansia muciniphila and Parabacteroides distasonis were significantly increased in the microbiota of resistant mice. To causally connect these microbes to protection against disease, we colonized susceptible mice with the two bacterial species. Our results demonstrate that A. muciniphila and P. distasonis synergistically drive a protective effect in both acute and chronic models of colitis by boosting the frequency of type 3 innate lymphoid cells in the colon and by improving gut epithelial integrity. Altogether, our work reveals a combined effort of commensal microbes in offering protection against severe intestinal inflammation by shaping gut immunity and by enhancing intestinal epithelial barrier stability. Our study highlights the beneficial role of gut bacteria in dictating intestinal homeostasis, which is an important step toward employing microbiome-driven therapeutic approaches for IBD clinical management.

IMPORTANCE

The contribution of the gut microbiome to the balance between homeostasis and inflammation is widely known. Nevertheless, the etiology of inflammatory bowel disease, which is known to be influenced by genetics, immune response, and environmental cues, remains unclear. Unlocking novel players involved in the dictation of a protective gut, namely, in the microbiota component, is therefore crucial to develop novel strategies to tackle IBD. Herein, we revealed a synergistic interaction between two commensal bacterial strains, Akkermansia muciniphila and Parabacteroides distasonis, which induce protection against both acute and chronic models of colitis induction, by enhancing epithelial barrier integrity and promoting group 3 innate lymphoid cells in the colonic mucosa. This study provides a novel insight on how commensal bacteria can beneficially act to promote intestinal homeostasis, which may open new avenues toward the use of microbiome-derived strategies to tackle IBD.

Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family

Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (Topt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to Topt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.

Manganese reductive dissolution coupled to Sb mobilization in contaminated shooting range soil

A "redox-stat" RMnR bioreactor was employed to simulate moderately reducing conditions (+ 420 mV) in Sb-contaminated shooting range soils for approximately 3 months, thermodynamically favoring Mn(IV) reduction. The impact of moderately reducing conditions on elemental mobilization (Mn, Sb, Fe) and speciation [Sb(III) versus Sb(V); Fe2+/Fe3+] was compared to a control bioreactor RCTRL without a fixed redox potential. In both bioreactors, reducing conditions were accompanied by an increase in effluent Sb(V) and Mn(II) concentrations, suggesting that Sb(V) was released through microbial reduction of Mn oxyhydroxide minerals. This was underlined by multiple linear regression analysis showing a significant (p < 0.05) relationship between Mn and Sb effluent concentrations. Mn concentration was the sole variable exhibiting a statistically significant effect on Sb in RMnR, while under the more reducing conditions in RCTRL, pH and redox potential were also significant. Analysis of the bacterial community composition revealed an increase in the genera Azoarcus, Flavisolibacter, Luteimonas, and Mesorhizobium concerning the initial soil, some of which are possible key players in the process of Sb mobilization. The overall amount of Sb released in the RMnR (10.40%) was virtually the same as in the RCTRL (10.37%), which underlines a subordinate role of anoxic processes, such as Fe-reductive dissolution, in Sb mobilization. This research underscores the central role of relatively low concentrations of Mn oxyhydroxides in influencing the fate of trace elements. Our study also demonstrates that bioreactors operated as redox-stats represent versatile tools that allow quantifying the contribution of specific mechanisms determining the fate of trace elements in contaminated soils. KEY POINTS: • "Redox-stat" reactors elucidate Sb mobilization mechanisms • Mn oxyhydroxides microbial reductive dissolution has a major role in Sb mobilization in soils under moderately reducing conditions • Despite aging the soil exhibited significant Sb mobilization potential, emphasizing persistent environmental effects.

Effects of Exercise on Gut Microbiota of Adults: A Systematic Review and Meta-Analysis

BACKGROUND

The equilibrium between gut microbiota (GM) and the host plays a pivotal role in maintaining overall health, influencing various physiological and metabolic functions. Emerging research suggests that exercise modulates the abundance and functionality of gut bacteria, yet the comprehensive effects on GM diversity remain to be synthesized.

OBJECTIVES AND DESIGN

The study aims to quantitatively examine the effect of exercise on the diversity of gut microbiota of adults using a systemic review and meta-analysis approach.

METHODS

PubMed, Ebsco, Embase, Web of Science, Cochrane Central Register of Controlled Trials, the China National Knowledge Infrastructure, and Wanfang Data were searched from their inception to September 2023. Exercise intervention studies with a control group that describe and compare the composition of GM in adults, using 16S rRNA gene sequencing, were included in this meta-analysis.

RESULTS

A total of 25 studies were included in this meta-analysis with a total of 1044 participants. Based on a fixed-effects model [Chi2 = 29.40, df = 20 (p = 0.08); I2 = 32%], the pooled analysis showed that compared with the control group, exercise intervention can significantly increase the alpha diversity of adult GM, using the Shannon index as an example [WMD = 0.05, 95% CI (0.00, 0.09); Z = 1.99 (p = 0.05)]. In addition, exercise interventions were found to significantly alter GM, notably decreasing Bacteroidetes and increasing Firmicutes, indicating a shift in the Firmicutes/Bacteroidetes ratio. The subgroup analysis indicates that females and older adults appear to exhibit more significant changes in the Shannon Index and observed OTUs.

CONCLUSIONS

Exercise may be a promising way to improve GM in adults. In particular, the Shannon index was significantly increased after exercise. Distinct responses in GM diversity to exercise interventions based on gender and age implicated that more research was needed.

Gut microbiota's influence on erysipelas: evidence from a two-sample Mendelian randomization analysis

Background

Previous studies have suggested a link between gut microbiota and skin diseases, including erysipelas, an inflammatory skin condition. Despite this, the precise nature of the relationship between erysipelas and gut microbiota remains unclear and subject to debate.

Methods

We conducted a Mendelian Randomization (MR) analysis using publicly available summary data from genome-wide association studies (GWAS) to explore the potential causal relationship between gut microbiota and erysipelas. Instrumental variables (IVs) were identified using a comprehensive set of screening methods. We then performed MR analyses primarily using the Inverse Variance Weighted (IVW) method, complemented by alternative approaches such as MR Egger, weighted median, simple mode, and weighted mode. A series of sensitivity analyses, including Cochran's Q test, MR-Egger intercept test, Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) test, and a leave-one-out test, were executed to ensure the robustness and validity of our findings.

Results

We identified potential associations between erysipelas and various gut microbiota, including Alcaligenaceae (OR 1.23; 95% CI 1.06-1.43; p=0.006), Rikenellaceae (OR 0.77; 95% CI 0.67-0.90; p=0.001), and others. Notably, associations with Actinomyces, Lachnospiraceae NC2004 group, Ruminiclostridium 9, Ruminococcaceae UCG014, Odoribacter, and Actinobacteria were also observed. Sensitivity analyses confirmed the robustness of these associations.

Conclusion

Our MR analysis suggests both potentially beneficial and harmful causal relationships between various gut microbiota and the incidence of erysipelas. This study provides new theoretical and empirical insights into the pathogenesis of erysipelas and underscores the potential for innovative preventive and therapeutic approaches.

Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis

BACKGROUND

Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis.

METHODS

By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs).

RESULTS

Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients.

CONCLUSIONS

We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC.

Gut microbiota-derived 5-hydroxyindoleacetic acid from pumpkin polysaccharides supplementation alleviates colitis via MAPKs-PPARγ/NF-κB inhibition

Polysaccharides from Pumpkin (Cucurbita moschata Duchesne) (PPs) have many pharmacological activities, including anti-oxidant, immune, and intestinal microbiota regulation. These activities have provided some reminders of its potential therapeutic effect on ulcerative colitis (UC), but this has not yet been confirmed. This study preliminarily confirmed its significant anti-UC activity superior to Salicylazosulfapyridine. The average molecular weight of PPs was 3.10 × 105 Da, and PPs mainly comprised Mannose, Rhamnose, Galacturonic acid, Galactosamine, Glucose, and Xylose with molar ratios of 1.58:3.51:34.54:1.00:3.25:3.02. PPs (50, 100 mg/kg) could significantly resist dextran sodium sulfate induced UC on C57BL/6 mice by improving gut microbiota dysbiosis, such as the changes of relative abundance of Bacteroides, Culturomica, Mucispirillum, Escherichia-Shigella, Alistipes and Helicobacter. PPs also reverse the abnormal inflammatory reaction, including abnormal level changes of TNF-α, IFN-γ, IL-1β, IL-4, IL-6, IL-10, and IL-18. Metabolomic profiling showed that PPs supplementation resulted in the participation of PPAR and MAPK pathways, as well as the increase of 5-hydroxyindole acetic acid (5-HIAA) level. 5-HIAA also exhibited individual and synergistic anti-UC activities in vivo. Furthermore, combination of PPs and 5-HIAA could also elevate the levels of PPARγ in nuclear and inhibit MAPK/NF-ĸB pathway in the colon. This study revealed that PPs and endogenous metabolite 5-HIAA might be developed to treat UC.

Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae

Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera 'Chryseosolibacter', 'Dawidia', and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.

Characterization of Solitalea canadensis α-mannosidase with specific activity towards α1,3-Mannosidic linkages

A recombinant exo-α-mannosidase from Solitalea canadensis (Sc3Man) has been characterized to exhibit strict specificity for hydrolyzing α1,3-mannosidic linkages located at the non-reducing end of glycans containing α-mannose. Enzymatic characterization revealed that Sc3Man operates optimally at a pH of 5.0 and at a temperature of 37 °C. The enzymatic activity was notably enhanced twofold in the presence of Ca2+ ions, emphasizing its potential dependency on this metal ion, while Cu2+ and Zn2+ ions notably impaired enzyme function. Sc3Man was able to efficiently cleave the terminal α1,3 mannose residue from various high-mannose N-glycan structures and from the model glycoprotein RNase B. This work not only expands the categorical scope of bacterial α-mannosidases, but also offers new insight into the glycan metabolism of S. canadensis, highlighting the enzyme's utility for glycan analysis and potential biotechnological applications.

Characterization and structural study of a novel β-N-acetylgalactosaminidase from Niabella aurantiaca

We report here the identification, characterization and three-dimensional (3D) structure determination of NaNga, a newly identified β-N-acetylgalactosaminidase from the Gram-negative soil bacterium Niabella aurantiaca DSM 17617. When recombinantly expressed in Escherichia coli, the enzyme selectively cleaved 4-nitrophenyl-N-acetyl-β-d-galactosamine (pNP-β-d-GalpNAc). The X-ray crystal structure of the protein was refined to 2.5 Å and consists of an N-terminal β-sandwich domain and a (β/α)8 barrel catalytic domain. Despite a mere 22% sequence identity, the 3D structure of NaNga is similar to those previously determined for family GH123 members, suggesting it also employs the same substrate-assisted catalytic mechanism. Inhibition by N-acetyl-galactosamine thiazoline (GalNAc-thiazoline) supports the suggested mechanism. A phylogenetic analysis of its proximal sequence space shows significant clustering of unknown sequences around NaNga with sufficient divergence with previously identified GH123 members to subdivide this family into distinct subfamilies. Although the actual biological substrate of our enzyme remains unknown, examination of the active site pocket suggests that it may be a β-N-acetylgalactosaminide substituted by a monosaccharide at O-3. Analysis of the genomic context suggests, in turn, that this substituted β-N-acetylgalactosaminide may be appended to a d-arabinan from an environmental Actinomycete.

Camellia oil exhibits anti-fatigue property by modulating antioxidant capacity, muscle fiber, and gut microbial composition in mice

Camellia seed oil (CO) has high nutritional value and multiple bioactivities. However, the specific anti-fatigue characteristics and the implied mechanism of CO have not yet been fully elucidated. Throughout this investigation, male C57BL/6J mice, aged 8 weeks, underwent exhaustive exercise with or without CO pretreatment (2, 4, and 6 mL/kg BW) for 28 days. CO could extend the rota-rod and running time, reduce blood urea nitrogen levels and serum lactic acid, and increase muscle and hepatic glycogen, adenosine triphosphate, and anti-oxidative indicators. Additionally, CO could upregulate the mRNA and Nrf2 protein expression levels, as well as enhance the levels of its downstream antioxidant enzymes and induce the myofiber-type transformation from fast to slow and attenuate the gut mechanical barrier. Moreover, CO could ameliorate gut dysbiosis by reducing Firmicutes to Bacteroidetes ratio at the phylum level, increasing the percentage of Alistipes, Alloprevotella, Lactobacillus, and Muribaculaceae, and decreasing the proportion of Dubosiella at the genus level. In addition, specific bacterial taxa, which were altered by CO, showed a significant correlation with partial fatigue-related parameters. These findings suggest that CO may alleviate fatigue by regulating antioxidant capacity, muscle fiber transformation, gut mechanical barrier, and gut microbial composition in mice. PRACTICAL APPLICATION: Our study revealed that camellia seed oil (CO) could ameliorate exercise-induced fatigue in mice by modulating antioxidant capacity, muscle fiber, and gut microbial composition in mice. Our results promote the application of CO as an anti-fatigue functional food that targets oxidative stress, myofiber-type transformation, and microbial community.

Alterations in gut microbiota and bile acids by proton-pump inhibitor use and possible mediating effects on elevated glucose levels and insulin resistance

Several observational studies have suggested that proton-pump inhibitor (PPI) use might increase diabetes risk, but the mechanism remains unclear. This study aimed to investigate the effects of PPI use on gut microbiota and bile acids (BAs) profiles, and to explore whether these changes could mediate the association of PPIs use with fasting blood glucose (FBG) levels and insulin resistance (IR) in Chinese population. A cross-sectional study was conducted in Shenzhen, China, from April to August 2021, enrolled 200 eligible patients from the local hospital. Participants completed a questionnaire and provided blood and stool samples. Gut microbiome was measured by16S rRNA gene sequencing, and bile acids were quantified by UPLC-MS/MS. Insulin resistance (IR) was assessed using the Homeostasis Model Assessment 2 (HOMA2-IR). PPI use was positively associated with higher levels of FBG and HOMA2-IR after controlling for possible confounders. PPI users exhibited a decreased Firmicutes and an increase in Bacteroidetes phylum, alongside higher levels of glycoursodeoxycholic acid (GUDCA) and taurochenodeoxycholic acid (TCDCA). Higher abundances of Bacteroidetes and Fusobacterium as well as higher levels of TCDCA in PPI users were positively associated with elevated FBG or HOMA2-IR. Mediation analyses indicated that the elevated levels of FBG and HOMA2-IR with PPI use were partially mediated by the alterations in gut microbiota and specific BAs (i.e., Fusobacterium genera and TCDCA). Long-term PPI use may increase FBG and HOMA2-IR levels, and alterations in gut microbiota and BAs profiles may partially explain this association.

The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond

The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.

Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice

BACKGROUND

Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored.

RESULTS

In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects.

CONCLUSIONS

Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.

Apple polyphenol extract ameliorates sugary-diet-induced depression-like behaviors in male C57BL/6 mice by inhibiting the inflammation of the gut-brain axis

To explore whether apple polyphenol extract (APE) ameliorates sugary-diet-induced depression-like behaviors, thirty male C57BL/6 mice (3-4 weeks old) were assigned to three groups randomly to receive different treatments for 8 consecutive weeks: (1) control group (CON), (2) S-HSD group (60% high sucrose diet feeding with 0.1 mg mL-1 sucralose solution as drinking water), and (3) S-APE group (S-HSD feeding with 500 mg per (kg bw day) APE solution gavage). The S-HSD group showed significant depression-like behaviors compared with the CON group, which was manifested by an increased number of buried marbles in the marble burying test, prolonged immobility time in both the tail suspension test and forced swimming test, and cognitive impairment based on the Morris water maze test. However, APE intervention significantly improved the depression-like behaviors by reducing serum levels of corticosterone and adrenocorticotropic hormone, and increasing the serum level of IL-10. Moreover, APE intervention inhibited the activation of the NF-κB inflammatory pathway, elevated colonic MUC-2 protein expression, and elevated the colonic and hippocampal tight junction proteins of occludin and ZO-1. Furthermore, APE intervention increased the richness and diversity of gut microbiota by regulating the composition of microbiota, with increased relative abundance of Firmicutes and Bacteroidota, decreased relative abundance of Verrucomicrobiota at the phylum level, significantly lowered relative abundance of Akkermansia at the genus level, and rebalanced abnormal relative abundance of Muribaculaceae_unclassified, Coriobacteriaceae_UCG-002, and Lachnoclostridium induced by S-HSD feeding. Thus, our study supports the potential application of APE as a dietary intervention for ameliorating depression-like behavioral disorders.

Stilbenes-enriched peanut sprouts alleviated physical fatigue via regulating interactions of nutrients-microbiota-metabolites revealed by multi-omics analysis

In this study, the antifatigue effect and mechanism of peanut sprouts were explored. BALB/c mice divided into three groups (control, dark and UV-C) were respectively supplemented with a normal diet, peanut sprouts (dark germination) added diet and stilbenes-enriched peanut sprouts (UV-C radiated germination) added diet. Results showed that swimming time and levels of blood glucose and antioxidant enzymes significantly increased, while contents of triglyceride and malondialdehyde notably decreased by peanut sprout supplementation. Besides, combined analysis of gut microbiota gene sequencing and targeted metabolomics of fecal metabolites revealed that peanut sprout supplementation up-regulated abundances and metabolic transformations of Catenibacillus, Odoribacter, Prevotellaceae-UCG-001 and Butyricicoccus while it down-regulated the abundance of Parabacteroides. Consequently, contents of sebacic acid, azelaic acid, suberic acid, heptanoic acid, pimelic acid, aminoadipic acid and mono-phenolics notably increased, which were markedly correlated with the antifatigue effect. Compared with the dark group, the swimming time, glutathione peroxidase activity, methylmalonylcarnitine content and abundances of Butyricicoccus, Catenibacillus and Lachnospiraceae NK4A136 were higher in the UV-C group, while opposite results were obtained for the levels of triglyceride, malondialdehyde, alpha-linolenic acid, gamma-linolenic acid, 10Z-heptadecenoic acid and palmitelaidic acid. Overall, peanut sprout supplementation could alleviate fatigue by modulating gut microbiota composition to promote fatty acid oxidation and lysine and stilbene catabolism to increase energy supply and regulate redox balance. UV-C-radiated peanut sprout supplementation could alleviate fatigue more effectively by up-regulating abundances of Butyricicoccus, Catenibacillus and Lachnospiraceae NK4A136 to promote long-chain fatty acid oxidation and catabolism of flavonoids and stilbenes efficiently.

Bacterial Contamination in the Different Parts of Household Washing Machine: New Insights from Chengdu, Western China

The moist and warm environment in the household washing machine provides ideal living conditions for the growth and survival of various microorganisms. However, the biodiversity of bacterial community in the different parts of washing machine from Chinese households has not been clarified. In this study, we assessed the bacterial communities in sealing strip, detergent drawer, inner drum, water filter and greywater of ten domestic washing machines quantitatively and qualitatively in Chengdu, southwestern China. The microbial cultivation results indicated that the washing machines from Chengdu had a severe microbial contamination reflected by large counts on bacteria, fungi and coliform. Furthermore, the sequencing data showed that the different parts displayed distinctive bacterial compositions. At the level of genus, the anaerobic bacteria of Caproiciproducens and Acidipropionibacterium were predominant in sealing strip. Barnesiella, Shinella and Sellimonas were detected as the characteristic bacteria in detergent drawer. The pathogens of Luteibacter and Corynebacterium at the genus level were the dominant bacteria in inner drum and water filter, respectively. The genera of Azospira, Roseococcus, Elstera and Aquicella, which belonged to the pathogenic phylum of Proteobacteria, were identified as bioindicators for the greywater. Gene function analysis on the sequencing data illustrated that the bacteria from washing machines were potentially associated with bacterial infectious diseases and antimicrobial resistance. This study shows the bacterial diversity in the different parts of washing machines, providing new clues for bacterial contamination in washing machines from Chinese households.

Alistipes indistinctus-derived hippuric acid promotes intestinal urate excretion to alleviate hyperuricemia

Hyperuricemia induces inflammatory arthritis and accelerates the progression of renal and cardiovascular diseases. Gut microbiota has been linked to the development of hyperuricemia through unclear mechanisms. Here, we show that the abundance and centrality of Alistipes indistinctus are depleted in subjects with hyperuricemia. Integrative metagenomic and metabolomic analysis identified hippuric acid as the key microbial effector that mediates the uric-acid-lowering effect of A. indistinctus. Mechanistically, A. indistinctus-derived hippuric acid enhances the binding of peroxisome-proliferator-activated receptor γ (PPARγ) to the promoter of ATP-binding cassette subfamily G member 2 (ABCG2), which in turn boosts intestinal urate excretion. To facilitate this enhanced excretion, hippuric acid also promotes ABCG2 localization to the brush border membranes in a PDZ-domain-containing 1 (PDZK1)-dependent manner. These findings indicate that A. indistinctus and hippuric acid promote intestinal urate excretion and offer insights into microbiota-host crosstalk in the maintenance of uric acid homeostasis.

The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

BACKGROUND

The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. However, there is still only limited knowledge on how the GM activity and metabolite production in the gastrointestinal tract could be influenced by pH and the pH gradient increases along the colon.

RESULTS

Here we investigate the effect of pH gradients corresponding to levels typically found in the colon on GM composition and metabolite production using substrates inulin, lactose, galactooligosaccharides (GOS), and fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) for each fecal inoculum and found that colonic pH gradients significantly influenced in vitro simulated GM structure, but the influence of fecal donor and substrate was more pronounced. Low pH regimes strongly influenced GM with the decreased relative abundance of Bacteroides spp. and increased Bifidobacterium spp. Higher in vitro simulated colonic pH promoted the production of SCFAs in a donor- and substrate-dependent manner. The butyrate producer Butyricimonas was enriched at higher pH conditions, where also butyrate production was increased for inulin. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae also increased at higher colonic pH, which was accompanied by increased production of propionate with GOS and FOS as substrates.

CONCLUSIONS

Together, our results show that colonic substrates such as dietary fibres influence GM composition and metabolite production, not only by being selectively utilized by specific microbes, but also because of their SCFA production, which in turn also influences colonic pH and overall GM composition and activity. Our work provides details about the effect of the gradients of rising pH from the proximal to distal colon on fermenting dietary substrates in vitro and highlights the importance of considering pH in GM research.

Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight

This study examined the interplay between bacterial and fungal communities in the human gut microbiota, impacting on nutritional status and body weight. Cohorts of 10 participants of healthy weight, 10 overweight, and 10 obese individuals, underwent comprehensive analysis, including dietary, anthropometric, and biochemical evaluations. Microbial composition was studied via gene sequencing of 16S and ITS rDNA regions, revealing bacterial (bacteriota) and fungal (mycobiota) profiles. Bacterial diversity exceeded fungal diversity. Statistically significant differences in bacterial communities were found within healthy-weight, overweight, and obese groups. The Bacillota/Bacteroidota ratio (previously known as the Firmicutes/Bacteroidetes ratio) correlated positively with body mass index. The predominant fungal phyla were Ascomycota and Basidiomycota, with the genera Nakaseomyces, Kazachstania, Kluyveromyces, and Hanseniaspora, inversely correlating with weight gain; while Saccharomyces, Debaryomyces, and Pichia correlated positively with body mass index. Overweight and obese individuals who harbored a higher abundance of Akkermansia muciniphila, demonstrated a favorable lipid and glucose profiles in contrast to those with lower abundance. The overweight group had elevated Candida, positively linked to simple carbohydrate consumption. The study underscores the role of microbial taxa in body mass index and metabolic health. An imbalanced gut bacteriota/mycobiota may contribute to obesity/metabolic disorders, highlighting the significance of investigating both communities.

Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia

A dataset comprising metagenomes of outpatients (n = 28) with acute leukemia (AL) and healthy controls (n = 14) was analysed to investigate the associations between gut microbiota composition and metabolic activity and AL. According to the results obtained, no significant differences in the microbial diversity between AL outpatients and healthy controls were found. However, significant differences in the abundance of specific microbial clades of healthy controls and AL outpatients were found. We found some differences at taxa level. The relative abundance of Enterobacteriaceae, Prevotellaceae and Rikenellaceae was increased in AL outpatients, while Bacteirodaceae, Bifidobacteriaceae and Lachnospiraceae was decreased. Interestingly, the abundances of several taxa including Bacteroides and Faecalibacterium species showed variations based on recovery time from the last cycle of chemotherapy. Functional annotation of metagenome-assembled genomes (MAGs) revealed the presence of functional domains corresponding to therapeutic enzymes including L-asparaginase in a wide range of genera including Prevotella, Ruminococcus, Faecalibacterium, Alistipes, Akkermansia. Metabolic network modelling revealed potential symbiotic relationships between Veillonella parvula and Levyella massiliensis and several species found in the microbiota of AL outpatients. These results may contribute to develop strategies for the recovery of microbiota composition profiles in the treatment of patients with AL.

Gut dysbiosis is linked to metabolic syndrome in obese Egyptian women: potential treatment by probiotics and high fiber diets regimen

Metabolic syndrome (MetS) is defined as a cluster of glucose intolerance, hypertension, dyslipidemia, and central obesity with insulin resistance. The role of gut microbiota in metabolic disorders is increasingly considered. To investigate the effects of probiotic supplements and hypocaloric high fiber regimen on MetS in obese Egyptian women. A longitudinal follow-up intervention study included 58 obese Egyptian women, with a mean age of 41.62 ± 10.70 years. They were grouped according to the criteria of MetS into 2 groups; 23 obese women with MetS and 35 ones without MetS. They followed a hypocaloric high fiber regimen weight loss program, light physical exercise, and received a probiotic supplement daily for 3 months. For each participating woman, blood pressure, anthropometric measurements, basal metabolic rate (BMR), dietary recalls, laboratory investigations, and microbiota analysis were acquired before and after 3 months of follow-up. After intervention by the probiotic and hypocaloric high fiber regimen and light exercise, reduction ranged from numerical to significant difference in the anthropometric parameters, blood pressure, and BMR was reported. All the biochemical parameters characterized by MetS decreased significantly at p ≤ 0.05-0.01. Before the intervention, results revealed abundant of Bacteroidetes bacteria over Firmicutes with a low Firmicutes/Bacteroidetes ratio. After the intervention, Log Lactobacillus, Log Bifidobacteria, and Log Bacteroidetes increased significantly in both groups, while Log Firmicutes and the Firmicutes/Bacteroidetes Ratio revealed a significant decrease. In conclusion, this study's results highlight a positive trend of probiotics supplementation with hypocaloric high-fiber diets in amelioration of the criteria of the Mets in obese Egyptian women.

Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes

We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.

Impact of epizootics on mussel farms: Insights into microbiota composition of Mytilus species

Outbreaks of marine mussel mortality on French farms could have different aetiologies. One of them implies Vibrio splendidus strains. Beyond the involvement of this pathogen, there is considerable evidence that diseases often result from interactions between several microbes and the host. In this study, we explored the bacterial communities associated with mussel species and the surrounding water collected from a mussel farm affected by mortalities. The microbiota of Mytilus edulis, Mytilus galloprovincialis and their hybrids displayed an abnormal abundance of Proteobacteria, in particular the genera Vibrio, Cobetia and Arcobacter. Despite the dysbiosis, the Mediterranean mussel showed a different microbiota profile with a higher richness and presence of the phylum Bacteroidetes. Bipartite network analyses at the level of bacteria families confirmed this finding and showed that the microbiomes of M. edulis and the hybrids tended to cluster together. In addition, injection of mussels with the virulent V. splendidus induced less mortality rate in M. galloprovincialis compared to the other Mytilus sp. suggesting a better resistance of the Mediterranean mussel to infection. Our findings point to a probable aetiology of pathobiome-mediated disease in mussels. To fully understand this phenomenon, more knowledge is needed on the roles of pathobiotic systems and their development during disease establishment.

Occurrence, characteristics, and microbial community of microplastics in anaerobic sludge of wastewater treatment plants

Wastewater treatment plants (WWTPs) usually contain microplastics (MPs) due to daily influents of domestic and municipal wastewater. Thus, the WWTPs act as a point source of MPs distribution in the environment due to their incapability to remove MPs completely. In this study, MPs occurrence and distribution in anaerobic sludge from WWTPs in different regions (Kaifeng "KHP", Jinan "JSP", and Lanzhou "LGP") were studied. Followed by MPs identification by microscopy and Fourier transform infrared (FTIR) spectrum. The microbial communities associated with anaerobic sludge and MPs were also explored. The results showed that MPs concentrations were 16.5, 38.5, and 17.2 particles/g of total solids (TS) and transparent MPs accounted for 49.1%, 58.5%, and 48.3% in KHP, JSP, and LGP samples, respectively. Fibers represented the most common shape of MPs in KHP (49.1%), JSP (56.0%), and LGP (69.0%). The FTIR spectroscopy indicated the predominance of polyethylene polymer in 1-5 mm MPs. The Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes were the abundant phyla in all anaerobic sludge. The bacterial genera in KHP and LGP were similar, in which Caldilinea (>23%), Terrimonas (>10%), and Ferruginibacter (>7%) formed the core bacterial genera. While Rhodococcus (15.3%) and Rhodoplanes (10.9%) were dominating in JSP. The archaeal genera Methanosaeta (>69%) and Methanobrevibacter (>10%) were abundant in KHP and LGP sludge. While Methanomethylovorans accounted for 90% of JSP. Acetyltransferase and hydratase were the major bacterial enzymes, while reductase was the key archaeal enzyme in all anaerobic sludge. This study provided the baseline for MPs distribution, characterization, and MPs associated microbes in WWTPs.

Extracellular polysaccharides from Sporidiobolus pararoseus alleviates rheumatoid through ameliorating gut barrier function and gut microbiota

Rheumatoid arthritis (RA) is becoming a prevalent autoimmune disease affecting people worldwide, necessitating the exploration of novel therapeutic approaches due to the associated adverse effects of conventional therapeutic drugs. Sporidiobolus pararoseus polysaccharide (SPP) has been shown to exhibit significant immune stimulation and antioxidant activities. In this study, we constructed a mouse model of type II collagen-induced arthritis (CIA) to investigate the effects and potential mechanisms of SPP intervention on RA. Results showed that SPP intervention alleviated the degree of ankle swelling, joint histopathologic changes, joint pathological score and the expression of serum-associated inflammatory mediators (such as IL-1β and IL-6). 16S rRNA sequencing results indicated that SPP intervention significantly remodeled the intestinal microbiota composition. In particular, SPP intervention significantly increased the relative abundance of beneficial bacteria (Parabacteroides, Bacteroides and Rikenellaceae_RC9_gut_group) with the potential to degrade fungal polysaccharides or produce short-chain fatty acids (SCFAs). The production of SCFAs (especially acetic acid, propionic acid and butyric acid) indeed increased significantly. These SCFAs played an important role in maintaining intestinal barrier function and regulating immune homeostasis, which helped reduce inflammatory responses and alleviate the symptoms of RA.

Advanced treatment of antibiotic-polluted wastewater by a consortium composed of bacteria and mixed cyanobacteria

This study constructed a cyanobacteria-bacteria consortium using a mixture of non-toxic cyanobacteria (Synechococcus sp. and Chroococcus sp.) immobilized in calcium alginate and native bacteria in wastewater. The consortium was used for the advanced treatment of sulfamethoxazole-polluted wastewater and the production of cyanobacterial lipid. Mixed cyanobacteria increased the abundances of denitrifying bacteria and phosphorus-accumulating bacteria as well as stimulated various functional enzymes in the wastewater bacterial community, which efficiently removed 70.01-71.86% of TN, 91.45-97.04% of TP and 70.72-76.85% of COD from the wastewater. The removal efficiency of 55.29-69.90% for sulfamethoxazole was mainly attributed to the upregulation of genes encoding oxidases, reductases, oxidoreductases and transferases in two cyanobacterial species as well as the increased abundances of Stenotrophomonas, Sediminibacterium, Arenimonas, Novosphingobium, Flavobacterium and Hydrogenophaga in wastewater bacterial community. Transcriptomic responses proved that mixed cyanobacteria presented an elevated lipid productivity of 33.90 mg/L/day as an adaptive stress response to sulfamethoxazole. Sediminibacterium, Flavobacterium and Exiguobacterium in the wastewater bacterial community may also promote cyanobacterial lipid synthesis through symbiosis. Results of this study proved that the mixed cyanobacteria-bacteria consortium was a promising approach for advanced wastewater treatment coupled to cyanobacterial lipid production.

Alterations in the diversity, composition and function of the gut microbiota in Uyghur individuals with sarcopenia

BACKGROUND

Research on the gut microbiota has emerged as a new direction for understanding pathophysiologic changes in diseases associated with aging, such as sarcopenia. Several studies have shown that there are differences in the gut microbiota between individuals with sarcopenia and without sarcopenia. However, these differences are not consistent across regions and ethnic groups, and additional research is needed.

METHODS

In this study, we collected fresh fecal samples from 31 Uyghur individuals with sarcopenia and 31 healthy controls. We used 16S rRNA sequencing to obtain fecal base sequences and analyzed the diversity, composition and function of the gut microbiota.

RESULTS

There was no significant difference in alpha diversity between the sarcopenia group and the healthy control group (P > 0.05). There was a significant difference in beta diversity between the groups (P < 0.05). In the sarcopenia group, the abundances of Alloprevotella, un_f_Prevotellaceae, Anaerovibrio, Prevotellaceae_NK3B31_group, Mitsuokella, Prevotella and Allisonella were lower than those in the heathy control group, and the abundances of Flavobacteriales, Flavobacteriaceae, Catenibacterium, Romboutsia, Erysipelotrichaceae_UCG-003, GCA-900066575, Lachnospiraceae_FCS020_group, and un_f_Flavobacteriaceae were higher than those in the heathy control group. Linear discriminant analysis effect size (LEfSe) revealed that the microbial species in the control group that were significantly different from those in the sarcopenia group were concentrated in the genus Alloprevotella, while the species in the sarcopenia group were concentrated in the genus Catenibacterium. Functional prediction analysis revealed that D-alanine, glycine, serine, and threonine metabolism and transcription machinery, among others, were enriched in the sarcopenia group, which indicated that metabolic pathways related to amino acid metabolism and nutrient transport may be regulated to varying degrees in the pathophysiological context of sarcopenia.

CONCLUSIONS

There were significant differences in the composition and function of the gut microbiota between Xinjiang Uyghur sarcopenia individuals and healthy individuals. These findings might aid in the development of probiotics or microbial-based therapies for sarcopenia in Uyhur individuals.

Effect of Lactiplantibacillus plantarum CCFM8661 on serum metabolites and gut microbiota in a lead-exposed population

In this study, we investigated the impact of Lactiplantibacillus plantarum (L. plantarum) CCFM8661 on the gut microbiota, and the serum and fecal metabolomes in lead (Pb)-exposed individuals. The volunteers recruited for this study were divided into two treatment groups, (i) the placebo (control) and (ii) the L. plantarum CCFM8661 treatment groups. The analysis revealed that probiotic intervention reversed some of the changes in Pb exposure-induced intestinal bacterial abundance, including the abundance of Parabacteroides, Bacteroides, Clostridiaceae, and Erysipelotrichaceae. An analysis of the fecal metabolome identified 26 differential metabolites involved in purine metabolism, unsaturated fatty acid metabolism, and other pathways. Serum metabolite analysis showed that L. plantarum CCFM8661 treatment altered the serum metabolite levels of various metabolic pathways, such as the glycerophospholipid, amino acid, and glutathione metabolism pathways. These results suggest that L. plantarum CCFM8661 may have beneficial effects on Pb-exposed populations by modulating the gut microbiota, host serum metabolism, and the metabolism of the gut microbiota.

The gut microbiome modulates the susceptibility to traumatic stress in a sex-dependent manner

Post-traumatic stress disorder (PTSD), a psychological condition triggered by exposure to extreme or chronic stressful events, exhibits a sex bias in incidence and clinical manifestations. Emerging research implicates the gut microbiome in the pathogenesis of PTSD and its roles in stress susceptibility. However, it is unclear whether differential gut microbiota contribute to PTSD susceptibility in male and female rats. Here, we utilized the single prolonged stress animal model and employed unsupervised machine learning to classify stressed animals into stress-susceptible subgroups and stress-resilient subgroups. Subsequently, using 16S V3-V4 rDNA sequencing, we investigated the differential gut microbiota alterations between susceptible and resilient individuals in male and female rats. Our findings revealed distinct changes in gut microbiota composition between the sexes at different taxonomic levels. Furthermore, the abundance of Parabacteroides was lower in rats that underwent SPS modeling compared to the control group. In addition, the abundance of Tenericutes in the stress-susceptible subgroup was higher than that in the control group and stress-resilient subgroup, suggesting that Tenericutes may be able to characterize stress susceptibility. What is particularly interesting here is that Cyanobacteria may be particularly associated with anti-anxiety effects in male rats. This study underscores sex-specific variations in gut microbiota composition in response to stress and sex differences should be taken into account when using macrobiotics for neuropsychiatric treatment, highlighting potential targets for PTSD therapeutic interventions.

Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling

The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.

Crosstalk between innate immunity and rumen-fecal microbiota under the cold stress in goats

The balance of the microbiome, which is sensitive to temperature changes, plays a crucial role in maintaining overall health and reducing the risk of diseases. However, the specific mechanisms by which immunity and microbiota interact to adapt to cold stress have yet to be addressed. In this study, Nanjiang Yellow goats were chosen as a model and sampled during the cold (winter, cold stress) and warm (spring) seasons, respectively. Analyses of serum immune factors, as well as the composition of rumen and fecal microbial communities, were conducted to explore the crosstalk between microbiota and innate immunity under cold stress. Significantly increased levels of IgA (P < 0.01) were observed in the cold season compared to the warm season. Conversely, the levels of IL-2 (P = 0.02) and IL-6 (P < 0.01) diminished under cold stress. However, no significant differences were observed in IgG (P = 0.89), IgM (P = 0.42), and IL-4 (P = 0.56). While there were no significant changes in the diversity of bacterial communities between the warm and cold seasons, positive correlations between serum IgA, IL-2, IL-6 concentrations and several genera were observed. Furthermore, the weighted gene co-expression network analysis indicated that the microbiota enriched in the MEbrown module positively correlated with IgA, while the microbiota enriched in the MEblue module positively correlated with IL-2 and IL-6. The strong correlation between certain probiotics, including Alistipes, Bacteroides, Blautia, and Prevotellaceae_UCG.004, and the concentration of IL-2, and IL-6 suggests their potential role in immunomodulatory properties. This study provides valuable insights into the crosstalk between microbial communities and immune responses under the challenge of cold stress. Further studies on the immunomodulatory properties of these probiotics would contribute to the development of strategies to enhance the stress resistance of animals for improved overall health and survival.

Comparison of gut microbiota profiles between patients suffering from elderly frailty syndrome and non-frail elderly individuals

BACKGROUND

Frailty syndrome is a state of increased vulnerability to stressors, marked by lowered physical strength and increased dependence on others. The well-established changes in gut microbiota associated with old age suggest a probable relationship between gut microbiota and frailty.

METHODS AND RESULTS

This study was aimed at finding the relationship between gut microbiota and frailty syndrome, by comparing the sociodemographic data and the gut microbiota profiles of 23 non-frail and 14 frail elderly individuals. We used the quantitative polymerase chain reaction method (qPCR) to determine the bacterial loads of Bifidobacteria, Lactobacillus, Bacteroidetes, Prevotella, and Escherichia coli in stool samples from test subjects. We discovered a significant increase in the bacterial load of Prevotella in frail elderly individuals aged 70 or above. Other bacterial loads and ratios were not significantly different between the two groups.

CONCLUSIONS

More comprehensive studies with larger sample sizes and encompassing a wider range of inflammation-related bacteria need to be performed to discover the existence and exact nature of these relations.

Effects of the alpine meadow in different phenological periods on rumen fermentation and gastrointestinal tract bacteria community in grazing yak on the Qinghai-Tibetan Plateau

BACKGROUND

In this study, we investigated the effects of alpine meadow in different phenological periods on ruminal fermentation, serum biochemical indices, and gastrointestinal tract microbes in grazing yak on the Qinghai-Tibetan Plateau. A total of eighteen female freely grazing yaks with an average age of 3 years old and a body weight of 130 ± 19 kg were selected. According to the plant phenological periods, yaks were randomly allocated to one of three treatments: (1) regreen periods group (RP, n = 6); (2) grassy periods group (GP, n = 6); and (3) hay periods group (HP, n = 6). At the end of the experiment, the blood, rumen fluids, and rectal contents were collected to perform further analysis.

RESULTS

The concentrations of total volatile fatty acid (TVFA), acetate, glucose (GLU), triglyceride (TG), cholesterol (CHO), high density lipoprotein (HDL), and low density lipoprotein (LDL) were higher in the GP group than in the HP group (P < 0.05). However, compared with the RP and GP groups, the HP group had higher concentrations of isobutyrate, isovalerate, valerate, and creatinine (CREA) (P < 0.05). The abundance of Prevotella in the rumen, and the abundances of Rikenellaceae_RC9_gut_group, Eubacterium_coprostanoligenes_group, and Prevotellaceae_UCG-004 in the gut were higher in the GP group compared with the HP group (P < 0.05). The HP had higher abundance of Eubacterium_coprostanoligenes_group in the rumen as well as the abundances of Romboutsia and Arthrobacter in the gut compared with the RP and GP groups (P < 0.05).

CONCLUSIONS

Based on the results of rumen fermentation, serum biochemical, differential biomarkers, and function prediction, the carbohydrate digestion of grazing yak would be higher with the alpine meadow regreen and grassy due to the gastrointestinal tract microbes. However, the risk of microbe disorders and host inflammation in grazing yak were higher with the alpine meadow wither.

The antioxidant strain Lactiplantibacillus plantarum AS21 and Clostridium butyricum ameliorate DSS-induced colitis in mice by remodeling the assembly of intestinal microbiota and improving gut functions

Probiotics are known for their beneficial effects on improving intestinal function by alleviating the gut microbial diversity. However, the influences of antioxidant lactic acid bacteria (LAB) and anti-inflammatory Clostridium butyricum (CB) on ameliorating enteritis remain unclear. In this study, we investigated the effects of the antioxidant strain Lactiplantibacillus plantarum AS21 and CB alone, or in combination on intestinal microbiota, barrier function, oxidative stress and inflammation in mice with DSS-induced colitis. All probiotic treatments relieved the pathological development of colitis by improving the integrity of the intestinal mucosal barrier and the length of the colon. The probiotics also suppressed inflammation and oxidative stress by improving gut short-chain fatty acids and inhibiting the p38-MAPK/NF-κB pathway in colon tissues. According to the meta-network analysis, three distinct modules containing sensitive OTUs of the gut bacterial community specific to the control, DSS and DSS + probiotics groups were observed, and unlike the other two modules, Lachnospiraceae and Clostridia dominated the sensitive OTUs in the DSS + probiotics group. In addition, administration of the present probiotics particularly increased antioxidant and anti-inflammatory microbes Muribaculaceae, Bifidobacterium, Prevotellaceae and Alloprevotella. Furthermore, combined probiotic strain treatment showed a more stable anti-colitis effect than a single probiotic strain. Collectively, the present probiotics exhibited protective effects against colitis by suppressing the inflammation and oxidative damage in the colon, improving the gut microbiota and their functions, and consequently preventing the gut leak. The results indicate that the combination of the antioxidant properties of LAB and the anti-inflammatory properties of CB as nutritional intervention and adjuvant therapy could be an effective strategy to prevent and alleviate colitis.

Seasonal dynamics response mechanism of benthic microbial community to artificial reef habitats

Artificial reefs (ARs) have been globally deployed to enhance and restore coastal resource and ecosystems. Microorganisms play an essential role in marine ecosystems, while the knowledge regarding the impact of ARs on microecology is still limited, particularly data concerning the response of benthic microbial community to AR habitats. In this study, the seasonal dynamics of benthic microbial community in AR and adjacent non-artificial reef (NAR) areas surrounding Xiaoshi Island were investigated with high-throughput sequencing technology. The results revealed that the diversity and structure of microbial community between AR and NAR both displayed pronounced seasonal dynamics. There was a greater influence of season factors on microbial communities than that of habitat type. The microbial communities in AR and NAR habitats were characterized by a limited number of abundant taxa (ranging from 5 to 12 ASVs) with high relative abundance (8.35-25.53%) and numerous rare taxa (from 5994 to 12412 ASVs) with low relative abundance (11.91%-24.91%). Proteobacteria, Bacteroidota and Desulfobacterota were the common predominant phyla, with the relative abundances ranging from 50.94% to 76.76%. A total of 52 biomarkers were discovered, with 15, 4, 6, and 27 biomarkers identified in spring, summer, autumn and winter, respectively. Co-occurrence network analysis indicated that AR displayed a more complex interaction pattern and higher susceptibility to external disturbances. Furthermore, the neutral model and βNTI analyses revealed that the assembly of microbial communities in both AR and NAR is significantly influenced by stochastic processes. This study could provide valuable insights into the impact of ARs construction on the benthic ecosystems and would greatly facilitate the development and implementation of the future AR projects.

A Gpr35-tuned gut microbe-brain metabolic axis regulates depressive-like behavior

Gene-environment interactions shape behavior and susceptibility to depression. However, little is known about the signaling pathways integrating genetic and environmental inputs to impact neurobehavioral outcomes. We report that gut G-protein-coupled receptor, Gpr35, engages a microbe-to-brain metabolic pathway to modulate neuronal plasticity and depressive behavior in mice. Psychological stress decreases intestinal epithelial Gpr35, genetic deletion of which induces depressive-like behavior in a microbiome-dependent manner. Gpr35-/- mice and individuals with depression have increased Parabacteroides distasonis, and its colonization to wild-type mice induces depression. Gpr35-/- and Parabacteroides distasonis-colonized mice show reduced indole-3-carboxaldehyde (IAld) and increased indole-3-lactate (ILA), which are produced from opposing branches along the bacterial catabolic pathway of tryptophan. IAld and ILA counteractively modulate neuroplasticity in the nucleus accumbens, a brain region linked to depression. IAld supplementation produces anti-depressant effects in mice with stress or gut epithelial Gpr35 deficiency. Together, these findings elucidate a gut microbe-brain signaling mechanism that underlies susceptibility to depression.

Metagenomic analysis of carbohydrate-active enzymes and their contribution to marine sediment biodiversity

Marine sediments constitute the world's most substantial long-term carbon repository. The microorganisms dwelling in these sediments mediate the transformation of fixed oceanic carbon, but their contribution to the carbon cycle is not fully understood. Previous culture-independent investigations into sedimentary microorganisms have underscored the significance of carbohydrates in the carbon cycle. In this study, we employ a metagenomic methodology to investigate the distribution and abundance of carbohydrate-active enzymes (CAZymes) in 37 marine sediments sites. These sediments exhibit varying oxygen availability and were isolated in diverse regions worldwide. Our comparative analysis is based on the metabolic potential for oxygen utilisation, derived from genes present in both oxic and anoxic environments. We found that extracellular CAZyme modules targeting the degradation of plant and algal detritus, necromass, and host glycans were abundant across all metagenomic samples. The analysis of these results indicates that the oxic/anoxic conditions not only influence the taxonomic composition of the microbial communities, but also affect the occurrence of CAZyme modules involved in the transformation of necromass, algae and plant detritus. To gain insight into the sediment microbial taxa, we reconstructed metagenome assembled genomes (MAG) and examined the presence of primary extracellular carbohydrate active enzyme (CAZyme) modules. Our findings reveal that the primary CAZyme modules and the CAZyme gene clusters discovered in our metagenomes were prevalent in the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. We compared those MAGs to organisms from the same taxonomic classes found in soil, and we found that they were similar in its CAZyme repertoire, but the soil MAG contained a more abundant and diverse CAZyme content. Furthermore, the data indicate that abundant classes in our metagenomic samples, namely Alphaproteobacteria, Bacteroidia and Gammaproteobacteria, play a pivotal role in carbohydrate transformation within the initial few metres of the sediments.

Temporal variations in the gut microbial diversity in response to high-fat diet and exercise

High-fat diet-induced obesity is a pandemic caused by an inactive lifestyle and increased consumption of Western diets and is a major risk factor for diabetes and cardiovascular diseases. In contrast, exercise can positively influence gut microbial diversity and is linked to a decreased inflammatory state. To understand the gut microbial variations associated with exercise and high-fat diet over time, we conducted a longitudinal study to examine the effect of covariates on gut microbial diversity and composition. Young mice were divided into four groups: Chow-diet (CHD), high-fat diet (HFD), high-fat diet + exercise (HFX), and exercise only (EXE) and underwent experimental intervention for 12 weeks. Fecal samples at week 0 and 12 were collected for DNA extraction, followed by 16S library preparation and sequencing. Data were analyzed using QIIME 2, R and MicrobiomeAnalyst. The Bacteroidetes-to-Firmicutes ratio decreased fivefold in the HFD and HFX groups compared to that in the CHD and EXE groups and increased in the EXE group over time. Alpha diversity was significantly increased in the EXE group longitudinally (p < 0.02), whereas diversity (Shannon, Faith's PD, and Fisher) and richness (ACE) was significantly reduced in the HFD (p < 0.005) and HFX (p < 0.03) groups over time. Beta diversity, based on the Jaccard, Bray-Curtis, and unweighted UniFrac distance metrics, was significant among the groups. Prevotella, Paraprevotella, Candidatus arthromitus, Lactobacillus salivarius, L. reuteri, Roseburia, Bacteroides uniformis, Sutterella, and Corynebacterium were differentially abundant in the chow-diet groups (CHD and EXE). Exercise significantly reduced the proportion of taxa characteristic of a high-fat diet, including Butyricimonas, Ruminococcus gnavus, and Mucispirillum schaedleri. Diet, age, and exercise significantly contributed to explaining the bacterial community structure and diversity in the gut microbiota. Modulating the gut microbiota and maintaining its stability can lead to targeted microbiome therapies to manage chronic and recurrent diseases and infections.

Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors

BACKGROUND

Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision.

RESULTS

Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota.

CONCLUSIONS

Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.

Unraveling the mystery: a Mendelian randomized exploration of gut microbiota and different types of obesity

Background

Numerous studies have demonstrated the influence of gut microbiota on the development of obesity. In this study, we utilized Mendelian randomization (MR) analysis to investigate the gut microbiota characteristics among different types of obese patients, aiming to elucidate the underlying mechanisms and provide novel insights for obesity treatment.

Methods

Two-sample multivariable Mendelian randomization (MR) analysis was employed to assess causal relationships between gut microbiota and various obesity subtypes. Gut microbiota data were obtained from the international consortium MiBioGen, and data on obese individuals were sourced from the Finnish National Biobank FinnGen. Eligible single-nucleotide polymorphisms (SNPs) were selected as instrumental variables. Various analytical methods, including inverse variance weighted (IVW), MR-Egger regression, weighted median, MR-RAPS, and Lasso regression, were applied. Sensitivity analyses for quality control included MR-Egger intercept tests, Cochran's Q tests, and leave-one-out analyses and others.

Results

Mendelian randomization studies revealed distinct gut microbiota profiles among European populations with different obesity subtypes. Following multivariable MR analysis, we found that Ruminococcaceae UCG010 [Odds Ratio (OR): 0.842, 95% confidence interval (CI): 0.766-0.926, Adjusted P value: 0.028] independently reduced the risk of obesity induced by excessive calorie intake, while Butyricimonas [OR: 4.252, 95% CI: 2.177-8.307, Adjusted P value: 0.002] independently increased the risk of medication-induced obesity. For localized adiposity, Pasteurellaceae [OR: 0.213, 95% CI: 0.115-0.395, Adjusted P value: <0.001] acted as a protective factor. In the case of extreme obesity with alveolar hypoventilation, lactobacillus [OR: 0.724, 95% CI: 0.609-0.860, Adjusted P value: 0.035] reduced the risk of its occurrence. Additionally, six gut microbiota may have potential roles in the onset of different types of obesity. Specifically, the Ruminococcus torques group may increase the risk of its occurrence. Desulfovibrio and Catenabacterium may serve as protective factors in the onset of Drug-induced obesity. Oxalobacteraceae, Actinomycetaceae, and Ruminiclostridium 9, on the other hand, could potentially increase the risk of Drug-induced obesity. No evidence of heterogeneity or horizontal pleiotropy among SNPs was found in the above studies (all P values for Q test and MR-Egger intercept > 0.05).

Conclusion

Gut microbiota abundance is causally related to obesity, with distinct gut microbiota profiles observed among different obesity subtypes. Four bacterial species, including Ruminococcaceae UCG010, Butyricimonas, Pasteurellaceae and lactobacillus independently influence the development of various types of obesity. Probiotic and prebiotic supplementation may represent a novel approach in future obesity management.

Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage

Sewer systems play vital roles in wastewater treatment facilities, and the microbial communities contribute significantly to the transformation of domestic wastewater. Therefore, this study conducted a 180-day experiment on a sewer system and utilized the high-throughput sequencing technology to characterize the microbial communities. Additionally, community assembly analysis was performed to understand the early-stage dynamics within the sewer system. The results demonstrated that the overall diversity of microbial communities exhibited fluctuations as the system progressed. The dominant phyla observed were Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, accounting for over 85.4% of the total relative abundances. At the genus level, bacteria associated with fermentation displayed a high relative abundance, particularly during days 75 to 180. A random-forest machine-learning model identified a group of microbes that confirmed the substantial contribution of fermentation. During the process of fermentation, microorganisms predominantly utilized propionate formation as the main pathway for acidogenesis, followed by acetate and butyrate formation. In terms of nitrogen and sulfur cycles, dissimilatory nitrate reduction and assimilatory sulfate reduction played significant roles. Furthermore, stochastic ecological processes had a dominant effect during the experiment. Dispersal limitation primarily governed the assembly process almost the entire experimental period, indicating the strong adaptability and metabolic plasticity of microorganisms in response to environmental variations. This experiment provides valuable insights into the metabolic mechanisms and microbial assembly associated with sewer systems.