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Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.

BackgroundSoybean cyst nematodes (SCN) as animal parasites of plants are not usually interested in killing the host but are rather focused on completing their life cycle to increase population, resulting in substantial yield losses. Remarkably, some agricultural soils after long-term crop monoculture show a significant decline in SCN densities and suppress disease in a sustainable and viable manner. However, relatively little is known about the microbes and mechanisms operating against SCN in such disease-suppressive soils.ResultsGreenhouse experiments showed that suppressive soils (S) collected from two provinces of China and transplantation soils (CS, created by mixing 10% S with 90% conducive soils) suppressed SCN. However, SCN suppressiveness was partially lost or completely abolished when S soils were treated with heat (80 °C) and formalin. Bacterial community analysis revealed that the specific suppression in S and CS was mainly associated with the bacterial phylum Bacteroidetes, specifically due to the enrichment of Chitinophaga spp. and Dyadobacter sp., in the cysts. SCN cysts colonized by Chitinophaga spp. showed dramatically reduced egg hatching, with unrecognizable internal body organization of juveniles inside the eggshell due to chitinase activity. Whereas, Dyadobacter sp. cells attached to the surface coat of J2s increased soybean resistance against SCN by triggering the expression of defence-associated genes. The disease-suppressive potential of these bacteria was validated by inoculating them into conducive soil. The Dyadobacter strain alone or in combination with Chitinophaga strains significantly decreased egg densities after one growing cycle of soybeans. In contrast, Chitinophaga strains alone required more than one growing cycle to significantly reduce SCN egg hatching and population density.ConclusionThis study revealed how soybean monoculture for decades induced microbiota homeostasis, leading to the formation of SCN-suppressive soil. The high relative abundance of antagonistic bacteria in the cyst suppressed the SCN population both directly and indirectly. Because uncontrolled proliferation will likely lead to quick demise due to host population collapse, obligate parasites like SCN may have evolved to modulate virulence/proliferation to balance these conflicting needs. Video Abstract.

A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron. From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a D-glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.

Hatcheries nationwide suffer from unexplained acute production failures, termed crashes. The microbiota of oysters relates to larval health with previous studies showing that some bacterial species have positive and others negative effects on oyster health. To investigate microbial correlates of crashes, we collected samples from every batch of oyster larvae (Crassostrea virginica) produced by the Horn Point Laboratory Oyster Hatchery since 2021 and analyzed the microbiota of 15 of those batches over their duration in the hatchery, from age of 3 to 5 days until either harvest or complete die off of the batch. Across events, die-offs generally became evident at or after six days of age. We found that the microbiota of oyster larvae appears to respond to die-off events with crashed batches having fundamentally different microbiota than good batches at age 7 to 9 and 9 to 12 days. Crashed batches were often taken over by microeukaryotes and bacterial taxa from the Protobacteria and Bacteroidetes phyla. However, this presumably opportunistic community differed between batches. Observed Vibrio species level groups did not appear to be oyster pathogens and appeared to respond to, rather than precede, crashes. The microbiota of 3 to 5 day old larvae were statistically related to whether a die-off occurred later in the larval batches' life, only when the taxa were first agglomerated to family level. The detection of two microbial species not previously known to associate with oysters, along with an increased presence of Dinophyceae, predominantly the toxin-producing Gyrodinium jinhaense, in 3 to 5 day old oyster larvae was statistically linked with subsequent batch crashes. This study suggests that the health of larval oysters shapes their microbiome. Conversely, it provides hints that the microbiome of larvae, and perhaps harmful algae, may drive hatchery crashes. [ABSTRACT FROM AUTHOR]

BACKGROUND: Human milk oligosaccharide (HMO) is a unique component of breastmilk. To date, no study has investigated the correlation between HMO and infant nutritional status particularly through the lens of gut microbiota. Therefore, our study aims to investigate the relationships between 2'-Fucosyllactose (2'-FL) in HMO and Firmicutes/Bacteroidetes (F/B) ratio among stunted infants. METHODS: A case-control study was conducted among 103 mother-infant pairs in Malang City, Indonesia. The quantification of 2'-FL HMO was assessed using High-Performance Liquid Chromatography (HPLC). The F/B ratio was analyzed with real-time poly-chain reaction (RT-PCR). For bivariate analysis, we employed the Spearman correlation and Mann--Whitney tests, while for multivariate analysis, we utilized multiple linear regression. RESULTS: The findings showed that the stunted nutritional status was detected in 49 out of 103 infants. In this group, 40.81% of mothers of infants with a stunted nutritional status had a secretor-positive status, while all mothers of infants with appropriate nutritional status tested positive for the secretor status (100%). However, the association between maternal secretor status and infant nutritional status was not statistically significant (p>0.05). The average levels of 2'-FL HMO in breast milk were lower in the group with stunted infants compared to non-stunted infants (1.21 mg/L vs 1.40 mg/L). The regression analysis revealed a significant association of 2'-FL HMO levels with the presence of Bacteroidetes and value of the F/B ratio (p>0.05). CONCLUSIONS: The breast milk component 2'-FL HMO significantly influences the gut microbiota of stunted infants. Future research aimed at elucidating the mechanisms by which 2'-FL HMO modulates infant gut microbiota should consider not only concentration and specific bacterial taxa but also intake levels [ABSTRACT FROM AUTHOR]

Background/Objectives: The phyla Firmicutes and Bacteroidetes are the main constituents of the gut microbiota. An imbalance in the gut microbiota is a sign of dysbiosis, and the Firmicutes-to-Bacteroidetes ratio has been proposed to be a marker of it, especially in the context of obesity. Since Croatia is the country with one of the highest obesity rates in Europe, a pilot observational study was conducted. The aim of the study was to investigate the validity of this potential biomarker in a methodological study using sample processing, DNA sequence analysis and characterization of recruited participants, including various health factors. Methods: A study involving Croatian population was conducted. Participants age, body weight, gender, health history and lifestyle factors were recorded. Gut microbiota composition was analyzed using 16S rRNA sequencing. The F/B ratio was calculated and evaluated in the context of health factors. Statistical analysis was performed to detect the possible association of F/B ratio and excess body weight (kg) and possible impact of certain lifestyle factors. Results: No association between the F/B ratio and excess body weight (kg) was found. Excess body weight was significantly associated with higher age, male gender, and history of appendectomy. No significant health predictors of the F/B ratio were found, but weight gain was positively associated with a higher average F/B ratio. Conclusions: Although this study could not confirm the predictive value of the F/B ratio or any other phyla-related biomarker for excess body weight in the study population, it demonstrated interesting insights into the obesity-associated gut microbiota. [ABSTRACT FROM AUTHOR]

Purpose: To determine the association of gut microbiome diversity and sight-threatening diabetic retinopathy (STDR) amongst patients with pre-existing diabetes. Methods: A cross-sectional study was performed, wherein 54 participants selected in total were placed into cases cohort if diagnosed with STDR and those without STDR but had a diagnosis of diabetes mellitus of at least 10-year duration were taken as controls. Statistical analysis comparing the gut microbial alpha diversity between cases and control groups as well as patients differentiated based on previously hypothesized Bacteroidetes/Firmicutes(B/F) ratio with an optimal cut-off 1.05 to identify patients with STDR were performed. Results: Comparing gut microbial alpha diversity did not show any difference between cases and control groups. However, statistically significant difference was noted amongst patients with B/F ratio ≥1.05 when compared to B/F ratio < 1.05; ACE index [Cut-off < 1.05:773.83 ± 362.73; Cut-off > 1.05:728.03 ± 227.37; p-0.016]; Chao1index [Cut-off < 1.05:773.63 ± 361.88; Cut-off > 1.05:728.13 ± 227.58; p-0.016]; Simpson index [Cut-off < 1.05:0.998 ± 0.001; Cut-off > 1.05:0.997 ± 0.001; p-0.006]; Shannon index [Cut-off < 1.05:6.37 ± 0.49; Cut-off > 1.05:6.10 ± 0.43; p-0.003]. Sub-group analysis showed that cases with B/F ratio ≥ 1.05, divided into proliferative diabetic retinopathy (PDR) and clinically significant macular edema (CSME), showed decreased diversity compared to controls (B/F ratio < 1.05). For PDR, all four diversity indices significantly decreased (p < 0.05). However, for CSME, only Shannon and Simpson indices showed significant decrease in diversity (p < 0.05). Conclusions: Based on clinical diagnosis, decreasing gut microbial diversity was observed among patients with STDR, although not statistically significant. When utilizing B/F ratio, the decreasing gut microbial diversity in STDR patients seems to be associated due to species richness and evenness in PDR when compared to decreasing species richness in CSME. [ABSTRACT FROM AUTHOR]

Microbial communities play a crucial role in the physiology of animal hosts; however, little is known about bacterial symbionts with the group cephalopods, specifically octopuses, and the function of these symbionts. The goal of this study was to determine if octopuses have a unique skin microbiome. The skin microbiome of two sympatric octopuses (Octopus vulgaris and Macrotritopus defilippi) was compared with the surrounding environment, sediment and seawater, to determine if octopus have a unique skin microbiome. High throughput sequencing of the bacterial 16S rRNA gene (V3-V4 region) amplicons was performed using an Illumina MiSeq. Sediment showed the greatest alpha diversity followed by octopus then seawater. Beta diversity revealed a difference in microbial composition between the octopus skin microbiome and sediment and seawater. While phylum Bacteroidetes appeared rare in environmental samples, it was most abundant for the octopus skin microbiome with the majority of the bacteria comprising the family Flavobacteriaceae. Proteobacteria, the largest group of bacteria, also constituted the octopus skin microbiome. Many of these groups occur on both octopus species; however, certain taxa differed in relative abundance between octopus species and may show species-specific host selection. Several bacteria that were identified for the octopus skin microbiome have been isolated from other marine animal hosts, identified as biodegraders and/ or produce pigments and squalene, or act as predators of other bacteria. These groups may play a role in defense against environmental stressors or pathogenic bacteria. This is the first study to characterize the skin microbiome in two wild sympatric octopuses. Due to the importance of bacterial symbionts, this can provide insight to the physiology, behavior, ecology, and ultimately the health of these important animals in marine environments as well as care in captive or laboratory settings. [ABSTRACT FROM AUTHOR]

Objective To investigate whether there is a causal relationship between gut microbiota and autism in children using the Mendelian randomization (MR) analysis method. Methods Genetic data from 18 340 individuals collected by the MiBioGen consortium across 24 cohorts were utilized. Reliable instrumental variables were constructed by selecting genetic variations associated with 33 microbial taxa. Using results from a genome-wide association study (GWAS) on susceptibility genes for autism in children conducted in Europe, we comprehensively assessed the causal link between gut microbiota and autism using inverse variance weighting (IVW), MR-Egger regression, and weighted median estimation (WME). Results Among the three selected single nucleotide polymorphisms (SNPs), the abundance of Bacteroidetes was significantly associated with autism (OR=0.508, 95%CI: 0.267-0.966, P=0.039). The IVW results indicated that for every one standard deviation increase in Bacteroidetes abundance, the average risk of developing autism decreased by 49.2%. Conclusion This study suggests a negative causal effect of Bacteroidetes abundance on the risk of developing autism in children. [ABSTRACT FROM AUTHOR]

We previously demonstrated that lipopolysaccharide (LPS) injection-induced immune stress could impair muscle growth in weaned piglets, but the precise mechanisms behind this remain elusive. Here, we found that chronic immune stress induced by LPS resulted in a significant reduction of 36.86% in the total muscle mass of piglets at 5 d post-treatment compared with the control group. At 1 d, prior to muscle mass loss, multiple alterations were noted in response to LPS treatment. These included a reduction in the abundance of Bacteroidetes, an increase in serum concentrations of pro-inflammatory cytokines, compromised mitochondrial morphology, and an upregulation in the expression of dynamin-related protein 1 (Drp1), a critical protein involved in mitochondrial fission. We highlight a strong negative correlation between Bacteroidetes abundance and the levels of serum pro-inflammatory cytokines, corroborated by in vivo intervention strategies in the musculature of both pig and mouse models. Mechanistically, the effects of Bacteroidetes on inflammation and muscle mass loss may involve the signaling pathway of the tauro-β-muricholic acid-fibroblast growth factor 15. Furthermore, the induction of overexpression of inflammatory cytokines, achieved without LPS treatment through oral administration of recombinant human IL-6 (rhIL-6), led to increased levels of circulating cytokines, subsequently causing a decrease in muscle mass. Notably, pre-treatment with Mdivi-1, an inhibitor of Drp-1, markedly attenuated the LPS-induced elevation in reactive oxygen species levels and rescued the associated decline in muscle mass. Collectively, these data indicate that LPS-induced muscle mass loss was linked to the reduction of Bacteroidetes abundance, increased inflammation, and the disruption of mitochondrial morphology. These insights offer promising avenues for the identification of potential therapeutic targets aimed at mitigating muscle mass loss. [ABSTRACT FROM AUTHOR]

Abstract Purpose To determine the association of gut microbiome diversity and sight-threatening diabetic retinopathy (STDR) amongst patients with pre-existing diabetes. Methods A cross-sectional study was performed, wherein 54 participants selected in total were placed into cases cohort if diagnosed with STDR and those without STDR but had a diagnosis of diabetes mellitus of at least 10-year duration were taken as controls. Statistical analysis comparing the gut microbial alpha diversity between cases and control groups as well as patients differentiated based on previously hypothesized Bacteroidetes/Firmicutes(B/F) ratio with an optimal cut-off 1.05 to identify patients with STDR were performed. Results Comparing gut microbial alpha diversity did not show any difference between cases and control groups. However, statistically significant difference was noted amongst patients with B/F ratio ≥1.05 when compared to B/F ratio 1.05:728.03 ± 227.37; p-0.016]; Chao1index [Cut-off 1.05:728.13 ± 227.58; p-0.016]; Simpson index [Cut-off 1.05:0.997 ± 0.001; p-0.006]; Shannon index [Cut-off 1.05:6.10 ± 0.43; p-0.003]. Sub-group analysis showed that cases with B/F ratio ≥ 1.05, divided into proliferative diabetic retinopathy (PDR) and clinically significant macular edema (CSME), showed decreased diversity compared to controls (B/F ratio

Haiyan Chen,1 Jiamin Cao,2 Feng Zhang,2 Wei Xiong2 1Wuzhou Workers Hospital, Wuzhou, Guangxi Zhuang, People’s Republic of China; 2Department of Ophthalmology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, People’s Republic of ChinaCorrespondence: Wei Xiong, Department of Ophthalmology, Third Xiangya Hospital, Central South University, Yuelu District, 138 Tongzipo Road, Changsha, Hunan, 410013, People’s Republic of China, Tel +86 13808469035, Email weixiong420@csu.edu.cnAbstract: Growing research proves gut microbiota and thyroid autoimmunity are linked. Graves’ disease (GD), as an autoimmune thyroid disease (AITD), is attributed to the production of thyroid-stimulating hormone receptor (TSHR) autoantibodies that bind to the thyroid follicular endothelial cells. It is well known that genetic factors, environmental factors, and immune disorders count for much in the development of GD. So far, the pathogenesis of GD is not elucidated. Emerging research reveals that the change in gut microbiota composition and its metabolites are related to GD. The gut microbial diversity is reduced in GDs compared with healthy controls (HCs). Firmicutes and Bacteroidetes account for a large proportion at the genus level. It is found that phyla Bacteroidetes increased while phyla Firmicutes decreased in Graves’ Disease patients (GD patients). Moreover, gut microbiota modulates the immune system to produce cytokines through bacterial metabolites. This article aims to find out the relation between gut microbiota dysbiosis and the development of GD. As more molecular pathways of bacterial metabolites are revealed, targeting microbiota is expected to the treatment of GD.Keywords: Graves’ Disease, gut microbiota, autoimmunity, dysbiosis, Firmicutes, bacteroidetes

BACKGROUND: The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability in gut microbiota. In a previous study, mouse strain-specific responses to American and ketogenic diets were observed along with several QTLs for metabolic traits. In the current study, we searched for genetic variants underlying differences in the gut microbiota in response to American and ketogenic diets, which are high in fat and vary in carbohydrate composition, between C57BL/6 J (B6) and FVB/NJ (FVB) mouse strains. RESULTS: Genetic mapping of microbial features revealed 18 loci under the QTL model (i.e., marginal effects that are not specific to diet or sex), 12 loci under the QTL by diet model, and 1 locus under the QTL by sex model. Multiple metabolic and microbial features map to the distal part of Chr 1 and Chr 16 along with eigenvectors extracted from principal coordinate analysis of measures of β-diversity. Bilophila, Ruminiclostridium 9, and Rikenella (Chr 1) were identified as sex- and diet-independent QTL candidate keystone organisms, and Parabacteroides (Chr 16) was identified as a diet-specific, candidate keystone organism in confirmatory factor analyses of traits mapping to these regions. For many microbial features, irrespective of which QTL model was used, diet or the interaction between diet and a genotype were the strongest predictors of the abundance of each microbial trait. Sex, while important to the analyses, was not as strong of a predictor for microbial abundances. CONCLUSIONS: These results demonstrate that sex, diet, and genetic background have different magnitudes of effects on inter-individual differences in gut microbiota. Therefore, Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation will be important to predict response to diets varying in carbohydrate composition. Video Abstract.

Abstract Background Propionate is a food preservative and platform chemical, but no biological process competes with current petrochemical production routes yet. Although propionate production has been described for gut bacteria of the class Bacteroidia, which also carry great capacity for the degradation of plant polymers, knowledge on propionate yields and productivities across species is scarce. This study aims to compare propionate production from glucose within Bacteroidia and characterize good propionate producers among this group. Results We collected published information on propionate producing Bacteroidia, and selected ten species to be further examined. These species were grown under defined conditions to compare their product formation. While propionate, acetate, succinate, lactate and formate were produced, the product ratios varied greatly among the species. The two species with highest propionate yield, B. propionicifaciens (0.39 gpro/ggluc) and B. graminisolvens (0.25 gpro/ggluc), were further examined. Product formation and growth behavior differed significantly during CO2-limited growth and in resting cells experiments, as only B. graminisolvens depended on external-added NaHCO3, while their genome sequences only revealed few differences in the major catabolic pathways. Carbon mass and electron balances in experiments with resting cells were closed under the assumption that the oxidative pentose pathway was utilized for glucose oxidation next to glycolysis in B. graminisolvens. Finally, during pH-controlled fed-batch cultivation B. propionicifaciens and B. graminisolvens grew up to cell densities (OD600) of 8.1 and 9.8, and produced 119 mM and 33 mM of propionate from 130 and 105 mM glucose, respectively. A significant production of other acids, particularly lactate (25 mM), was observed in B. graminisolvens only. Conclusions We obtained the first broad overview and comparison of propionate production in Bacteroidia strains. A closer look at two species with comparably high propionate yields, showed significant differences in their physiology. Further studies may reveal the molecular basis for high propionate yields in Bacteroidia, paving the road towards their biotechnological application for conversion of biomass-derived sugars to propionate.

Objective: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC. Methods: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed. Results: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable. Conclusion: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria. [ABSTRACT FROM AUTHOR]

An arsenate reductase (Car1) from the Bacteroidetes species Rufibacter tibetensis 1351T was isolated from the Tibetan Plateau. The strain exhibits resistance to arsenite [As(III)] and arsenate [As(V)] and reduces As(V) to As(III). Here we shed light on the mechanism of enzymatic reduction by Car1. AlphaFold2 structure prediction, active site energy minimization, and steady‐state kinetics of wild‐type and mutant enzymes give insight into the catalytic mechanism. Car1 is structurally related to calcineurin‐like metallophosphoesterases (MPPs). It functions as a binuclear metal hydrolase with limited phosphatase activity, particularly relying on the divalent metal Ni2+. As an As(V) reductase, it displays metal promiscuity and is coupled to the thioredoxin redox cycle, requiring the participation of two cysteine residues, Cys74 and Cys76. These findings suggest that Car1 evolved from a common ancestor of extant phosphatases by incorporating a redox function into an existing MPP catalytic site. Its proposed mechanism of arsenate reduction involves Cys74 initiating a nucleophilic attack on arsenate, leading to the formation of a covalent intermediate. Next, a nucleophilic attack of Cys76 leads to the release of As(III) and the formation of a surface‐exposed Cys74‐Cys76 disulfide, ready for reduction by thioredoxin. [ABSTRACT FROM AUTHOR]

A novel coupling process to replace the traditional multi-stage anammox process—sulfur autotrophic denitrification (SAD) coupled anaerobic ammonium oxidation (anammox) system was designed, which solved problems of nitrate produced in anammox process and low nitrate conversion rate caused by nitrite accumulation in SAD process. Different filter structures (SAD filter and anammox granular sludge) were investigated to further explore the excellent performance of the novel integrated reactor. The results of sequential batch experiments indicated that nitrite accumulation occurred during SAD, which inhibited the conversion of nitrate to dinitrogen gas. When SAD filter and anammox granular sludge were added to packed bed reactor simultaneously, the nitrate removal rate increased by 37.21% and effluent nitrite concentration decreased by 100% compared to that achieved using SAD. The stratified filter structure solved groove flow. Different proportion influence of SAD filter and anammox granular sludge on the stratified filter structure was evaluated. More suitable ratio of SAD filter to anammox granular sludge was 2:1. Proteobacteria (57.26%), Bacteroidetes (20.12%) and Chloroflexi (9.95%) were the main phyla. The dominant genera of denitrification functional bacteria were Thiobacillus (39.80%), Chlorobaculum (3.99%), norank_f_PHOs-HE36 (2.90%) and Ignavibacterium (2.64%). The dominant genus of anammox bacterium was Candidatus_Kuenenia (3.05%). [ABSTRACT FROM AUTHOR]

Background: Propionate is a food preservative and platform chemical, but no biological process competes with current petrochemical production routes yet. Although propionate production has been described for gut bacteria of the class Bacteroidia, which also carry great capacity for the degradation of plant polymers, knowledge on propionate yields and productivities across species is scarce. This study aims to compare propionate production from glucose within Bacteroidia and characterize good propionate producers among this group. Results: We collected published information on propionate producing Bacteroidia, and selected ten species to be further examined. These species were grown under defined conditions to compare their product formation. While propionate, acetate, succinate, lactate and formate were produced, the product ratios varied greatly among the species. The two species with highest propionate yield, B. propionicifaciens (0.39 gpro/ggluc) and B. graminisolvens (0.25 gpro/ggluc), were further examined. Product formation and growth behavior differed significantly during CO2-limited growth and in resting cells experiments, as only B. graminisolvens depended on external-added NaHCO3, while their genome sequences only revealed few differences in the major catabolic pathways. Carbon mass and electron balances in experiments with resting cells were closed under the assumption that the oxidative pentose pathway was utilized for glucose oxidation next to glycolysis in B. graminisolvens. Finally, during pH-controlled fed-batch cultivation B. propionicifaciens and B. graminisolvens grew up to cell densities (OD600) of 8.1 and 9.8, and produced 119 mM and 33 mM of propionate from 130 and 105 mM glucose, respectively. A significant production of other acids, particularly lactate (25 mM), was observed in B. graminisolvens only. Conclusions: We obtained the first broad overview and comparison of propionate production in Bacteroidia strains. A closer look at two species with comparably high propionate yields, showed significant differences in their physiology. Further studies may reveal the molecular basis for high propionate yields in Bacteroidia, paving the road towards their biotechnological application for conversion of biomass-derived sugars to propionate. [ABSTRACT FROM AUTHOR]

Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2–3 μm). The community from early March was typical for this season, with Alpha‐ and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Toward summer, Bacteroidetes, and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB‐dependent transporters of iron‐siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. This cheating ability of the Bacteroidetes may have contributed to their dominance in the summer. [ABSTRACT FROM AUTHOR]

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, nonlithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation). [ABSTRACT FROM AUTHOR]

Bioaerosols are a potential risk of infection in densely populated indoor sites at university campuses. In this study, indoor bioaerosols from the canteen, classroom, and dormitory on campus were sampled and analyzed in the summer of 2021 to investigate the harmful risk. The results showed that bacteria are the predominant microbes, and the total number of bacteria detected in the classroom during no lesson in the morning (33% of samples) and in the canteen during meal times (55% of samples) was greater than the World Health Organization's recommended value (1000 CFU/m3). The ranges of respirable bioaerosol (<3.3 µm) contributions in the classroom, dormitory, and canteen were 50–75%, 57–70%, and 64–80%, respectively. Bacteroidetes and Firmicutes were the most dominant phyla in all three indoor environments, with a relative abundance of both above 20%. At the family level, Muribaculaceae, Lachnospiraceae, and Bacteroidaceae had high relative abundance in all indoor sites. Some of the microbes carried by bioaerosols were conditionally pathogenic bacteria, such as Micrococcaceae and Enterococcaceae, which may have a harmful risk of causing various inflammatory infections. The results of this study provide basic data to improve indoor environments and control indoor bioaerosol pollution on campus. [ABSTRACT FROM AUTHOR]

Background and Objectives: TB infection is one of the most challengeable epidemiological issues. Complex interactions between microbiota and TB infection have been demonstrated. Alteration in microbial population during TB infection may act as a useful biomarker. The present study examined the microbiota patterns of blood and sputum samples collected from Afghan immigrants and Iranian patients with active TB. Materials and Methods: Sixty active pulmonary TB patients were enrolled in the study. Blood and sputum samples were collected. To detect phylum bacterial composition in the blood and sputum samples, bacterial 16S rRNA quantification by Real-Time qPCR was performed. Results: A significant decrease in Bacteroidetes in Iranian sputum and blood samples of Afghan immigrants and Iranian TB active subjects were seen. While, sputum samples of Afghan immigrants showed no significant differences in Bacteroidetes abundance among TB active and control. Firmicutes were also presented no significant difference between sputum samples of the two races. Actinobacteria showed a significant increase in Iranian and Afghan sputum samples while this phylum showed no significant abundance in Iranian and Afghan TB positive blood samples. Proteobacteria also showed an increase in sputum and blood samples of the two races. Conclusion: An imbalance in Bacteroidetes and Firmicutes abundance may cause an alteration in the microbiota composition, resulting in dysregulated immune responses and resulting in the augmentation of opportunistic pathogens during TB infection, notably Proteobacteria and Actinobacteria. Evaluation of human microbiota under different conditions of TB infection can be critical to a deeper understanding of the disease control. [ABSTRACT FROM AUTHOR]

The human gut has a rich and dynamic microbial population that plays an important role in many physiological activities. This review explores the complex interaction between the gut microbiota and human health, with an emphasis on its effect on neurodegenerative illnesses. The makeup of the gut microbiome and its impact on brain function through the gut–brain axis is highlighted. Dysbiosis, characterized by changes in the gut microbiota's composition, has been linked to the development of neurodegenerative diseases such as Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis. A Bidirectional communication between the stomach and the brain takes place via a variety of channels, including neurotransmitters and metabolites generated by gut bacteria. We investigate the processes through which dysbiosis causes neuroinflammation, oxidative stress, and neuronal damage, which drive disease development. Potential therapeutic approaches that focus on the gut microbiota, such as antibiotics, probiotics, prebiotics, and fecal microbiota transplantation, are reviewed, with promising preclinical and clinical findings. Overall, this study emphasizes the relevance of gut microbiota to neurodegenerative illnesses, as well as the need to understand and target the gut-brain axis for future treatment options. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the disruption of the swine gut microbiota and histopathological changes caused by infection with enterotoxigenic E. coli. Fecal samples were collected from piglets suffering from diarrhea post-recovery and healthy animals. Intestinal tissues were collected for histopathological changes. The results revealed histopathological changes mainly in the ileum of the infected animals compared to those in the ileum of the control and recovered animals. The operational taxonomic units (OTUs) revealed that the E. coli diarrheal group exhibited the highest bacterial richness. Principal coordinate analysis (PCoA) corroborated the presence of dysbiosis in the gut microbiota following E. coli-induced diarrhea. While the normal control and infected groups displayed slight clustering, the recovery group formed a distinct cluster with a distinct flora. Bacteroidetes, Firmicutes, and Fusobacteria were the dominant phyla in both the healthy and recovered piglets and in the diarrheal group. LEfSe and the associated LDA score analysis revealed that the recovered group exhibited dominance of the phyla Euryarchaeota and Bacteroidota, while groups N and I showed dominance of the phyla Firmicutes and Fusobacteriota, respectively. The LDA scores highlighted a significant expression of the Muribaculacea family in group R. The obtained findings will help in understanding the microbiome during swine colibacillosis, which will support control of the outbreaks. [ABSTRACT FROM AUTHOR]

In medicine, parasitic cysts (e.g., brain cysticerci) are believed to be sterile, and are primarily treated with antiparasitic medications, not antibiotics, which could prevent abscess formation and localized inflammation. This study quantified the microbial composition of parasitic cysts in a wild rodent, using multi-kingdom metagenomics to comprehensively assess if parasitic cysts are sterile, and further understand gut microbial translocation and adaptation in wildlife confined environments, outside the gut. Analysis was conducted on DNA from two hepatic parasitic cysts from a feline tapeworm, Hydatigera (Taenia) taeniaeformis, affecting a wild vole mouse (Microtus pennsylvanicus), and from feces, liver and peritoneal fluid of this and two other concurrent individual wild voles trapped during pest control in one of our university research vegetable gardens. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, Parabacteroides distasonis, Bacteroides (Bacteroidota); Klebsiella variicola, E. coli (Enterobacteriaceae); Enterococcus faecium and Lactobacillus acidophilus (Bacillota) inhabiting the cysts, and peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, and unexpectedly, a virus from the insect armyworm moth (Pseudaletia/Mythimna unipuncta), known as Mythimna unipuncta granulovirus A (MyunGV-A), in both cysts, and in one fecal and one peritoneal sample from the other non-cyst voles, indicating the survival and adaption potential of the insect virus in voles. Metagenomics also revealed a significantly lower probability of fungal detection in cysts compared to that in peritoneal fluid/feces (p < 0.05), with single taxon detection in each cyst (Malassezia and Pseudophaeomoniella oleicola). The peritoneal fluid had the highest probability for fungi. In conclusion, metagenomics revealed that bacteria/viruses/fungi coexist within parasitic cysts supporting the potential therapeutic benefits of antibiotics in cystic diseases, and in inflammatory microniches of chronic diseases, such as Crohn's disease gut wall cavitating micropathologies, from which we recently isolated similar synergistic pathogenic Bacteroidota and Enterobacteriaceae, and Bacillota. [ABSTRACT FROM AUTHOR]

Purpose: Evidence suggests that changes in the composition of gut microbiota may be linked to metabolic disorders including type 2 diabetes (T2D). The present study aims to evaluate the compositional changes of the intestinal microbiota in patients with T2D as compared to healthy individuals. Methods: In this case-control study, there were 18 T2D patients and 18 healthy individuals who served as controls. To profile the gut microbiota in both groups, bacterial DNA was extracted from fecal samples and analyzed using quantitative real-time polymerase chain reaction (qPCR). Results: The study discovered that diabetics had significantly greater frequencies of the genus Bacteroides and the phylum Bacteroidetes than did controls (P = 0.03 and P

Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.

The human gut has a rich and dynamic microbial population that plays an important role in many physiological activities. This review explores the complex interaction between the gut microbiota and human health, with an emphasis on its effect on neurodegenerative illnesses. The makeup of the gut microbiome and its impact on brain function through the gut–brain axis is highlighted. Dysbiosis, characterized by changes in the gut microbiota’s composition, has been linked to the development of neurodegenerative diseases such as Alzheimer’s, Parkinson’s, Huntington’s, and amyotrophic lateral sclerosis. A Bidirectional communication between the stomach and the brain takes place via a variety of channels, including neurotransmitters and metabolites generated by gut bacteria. We investigate the processes through which dysbiosis causes neuroinflammation, oxidative stress, and neuronal damage, which drive disease development. Potential therapeutic approaches that focus on the gut microbiota, such as antibiotics, probiotics, prebiotics, and fecal microbiota transplantation, are reviewed, with promising preclinical and clinical findings. Overall, this study emphasizes the relevance of gut microbiota to neurodegenerative illnesses, as well as the need to understand and target the gut-brain axis for future treatment options.

Particulate matter (PM) is the main air pollutant in China. Due to its wide distribution and difficulties in control, PM has been widely concerned. PM mainly enters human body through respiratory exposure and can cause a variety of health problems. Recent studies have shown that PM exposure is also associated with the occurrence and development of digestive system diseases, as it can enter human body indirectly through the respiratory tract or directly through the digestive tract. Gut microbiota (GM) is a group of microorganisms located in the intestinal epithelium mucosa and intestinal lumen. GM is large in number and rich in functions, and its homeostasis plays an important role in the intestinal health of individuals and even the health of the body. Because GM may mediate the health effects induced by environmental factors, more and more studies have focused on the effects of ambient PM on GM. In this review, we summarized the effects of a variety of ambient PM on GM homeostasis, focusing on five major phyla including Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobia, and discussed their main functions and the effects of PM on their homeostasis and abundance.

The aim of the study was to examine serum levels of liver and intestinal fatty acid-binding proteins (L-FABP and I-FABP), fecal numbers of Bacteroidetes (B) and Firmicutes (F) in patients with metabolic-associated fatty liver disease (MAFLD) in combination with type 2 diabetes mellitus (Т2DM) and small intestinal bacterial overgrowth (SIBO) syndrome. Materials and methods. The prospective, interventional, randomized study included 51 patients with MAFLD in combination with Т2DM, who were examined and divided into 2 groups. Group 1 consisted of 24 patients with MAFLD and Т2DM without SIBO. Group 2 was comprised of 27 patients with MAFLD in combination with Т2DM and SIBO. The control group included 20 apparently healthy individuals. Serum levels of L-FABP and I-FABP were measured by ELISA method using the Human L-FABP and I-FABP ELISA Kit test systems, respectively (Elabscience, USA). Fecal numbers of B and F were determined by real-time PCR. Bacterial DNA was detected in a thermal cycler Rotor-Gene 6000 (QIAGEN, Germany) using DNA 16S rRNA primers and NanoDrop ND-8000 reagents (Thermo Scientific, USA). Results. To assess the state of intestinal permeability, serum levels of L-FABP and I-FABP were examined and numbers of phylum F and В as well as their ratio were calculated. Patients of both groups have been found to have increased serum levels of L-FABP, I-FABP, numbers of B in fecal samples and decreased numbers of F and F/B ratio. Conclusions. The study results obtained have revealed increased intestinal permeability and demonstrated an important diagnostic value of serum L-FABP and I-FABP as a biomarker of intestinal permeability in diabetic MAFLD patients with or without SIBO. Increased fecal numbers of Bacteroidetes, decreased numbers of Firmicutes and F/B ratio have been detected in diabetic MAFLD patients with or without SIBO.

The rotating drum biofilter (RDB) was investigated as a biological process for purifying SO2 and NOx. After 25 days of film hanging, the inlet concentration was less than 2800 mg·m−3, and the NOx inlet concentration was less than 800 mg·m−3, with greater than 90% desulphurisation and denitration efficiency. Bacteroidetes and Chloroflexi were the dominant bacteria in desulphurisation, while Proteobacteria were the dominant bacteria in denitrification. The sulphur and nitrogen in RDB were balanced when the SO2 inlet concentration was 1200 mg·m−3 and the NOx inlet concentration was 1000 mg·m−3. The best results were obtained SO2-S removal load was 28.12 mg·L−1·h−1 and NOx-N removal load was 9.78 mg·L−1·h−1. when SO2 concentration was 1200 mg·m−3, NOx concentration was 800 mg·m−3, and empty bed retention time (EBRT) was 75.36 s. The liquid phase dominated the SO2 purification process, and the experimental data fit better with the liquid phase mass transfer model. NOx purification was governed by the biological and liquid phases, with the modified biological-liquid phase mass transfer model fitting the experimental data better. [ABSTRACT FROM AUTHOR]

Recent studies have begun exploring the potential involvement of microbiota in the pathogenesis of oral lichen planus (OLP), yet comprehensive investigations remain limited. Hence, this study aimed to compare the microbial profiles in saliva samples obtained from patients with OLP against those from healthy controls (HC), along with a comparison between erosive (E) and non-erosive (NE) OLP patients. Saliva samples were collected from 60 OLP patients (E: n = 25, NE: n = 35) and 30 HC individuals. Analysis revealed no significant differences in alpha diversity, as assessed by the Chao1 and Shannon index, across the three groups. However, Bray–Curtis distance analysis indicated a significant disparity in microbiome composition distribution between HC and E-OLP, as well as HC and NE-OLP groups. The six most abundant phyla observed across the groups were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Saccharibacteria (TM7). Notably, OLP groups exhibited a higher prevalence of Bacteroidetes. Prevotella emerged as the predominant genus in the OLP groups, while Capnocytophaga showed a relatively higher prevalence in E-OLP compared to NE-OLP. This study's findings indicate a notable difference in microbiota composition between HC and patients with OLP. Additionally, differences in the microbiome were identified between the E-OLP and NE-OLP groups. The increase in the proportion of certain bacterial species in the oral microbiome suggests that they may exacerbate the inflammatory response and act as antigens for OLP. [ABSTRACT FROM AUTHOR]

Pit mud (PM), as an important source of microorganisms, is necessary for Chinese strong-flavor baijiu (CSFB) production. Although it has been revealed that the PM prokaryotic community diversities are influenced by its quality, product area, ages, etc., the characteristics and assembly process of the prokaryotic community in PMs across a pH gradient are still unclear. In this study, the regular changes of α- and β-diversities of the prokaryotic community across a pH gradient in PMs were revealed, which could be divided into "stable", "relatively stable", and "drastically changed" periods. A total of 27 phyla, 53 classes, and 381 genera were observed in all given samples, dominated by Firmicutes, Bacteroidetes, Proteobacteria, Lactobacillus, Caproiciproducens, Proteiniphilum, etc. Meanwhile, the complexity of the network structure of the prokaryotic microbial communities is significantly influenced by pH. The community assembly was jointly shaped by deterministic and stochastic processes, with stochastic process contributing more. This study was a specialized report on elucidating the characteristics and assembly of PM prokaryotic communities across a pH gradient, and revealed that the diversity and structure of PM prokaryotic communities could be predictable, to some degree, which could contribute to expanding our understanding of prokaryotic communities in PM. [ABSTRACT FROM AUTHOR]

Multi-strain Limosilactobacillus (L.) fermentum is a potential probiotic with reported immunomodulatory properties. This study aimed to evaluate the composition, richness, and diversity of the gut microbiota in male and female rats after treatment with a multi-strain of L. fermentum at different doses. Thirty rats (fifteen male and fifteen female) were allocated into a control group (CTL), a group receiving L. fermentum at a dose of 108 CFU (Lf-108), and a group receiving L. fermentum at a dose of 1010 CFU (Lf-1010) for 13 weeks. Gut microbiota and serum cytokine levels were evaluated after L. fermentum treatment. Male CTL rats had a lower relative abundance of Bifidobacteriaceae and Prevotella and a lower alpha diversity than their female CTL counterparts (p < 0.05). In addition, male CTL rats had a higher Firmicutes/Bacteroidetes (F/B) ratio than female CTL rats (p < 0.05). In female rats, the administration of L. fermentum at 108 CFU decreased the relative abundance of Bifidobacteriaceae and Anaerobiospirillum and increased Lactobacillus (p < 0.05). In male rats, the administration of L. fermentum at 1010 CFU decreased the F/B ratio and increased Lachnospiraceae and the diversity of the gut microbiota (p < 0.05). The relative abundance of Lachnospiraceae and the alpha-diversity of gut microbiota were negatively correlated with serum levels of IL1β (r = −0.44) and TNFα (r = −0.39), respectively. This study identified important changes in gut microbiota between male and female rats and showed that a lower dose of L. fermentum may have more beneficial effects on gut microbiota in females, while a higher dose may result in more beneficial effects on gut microbiota in male rats. [ABSTRACT FROM AUTHOR]

The aim of the study was to examine serum levels of liver and intestinal fatty acid-binding proteins (L-FABP and I-FABP), fecal numbers of Bacteroidetes (B) and Firmicutes (F) in patients with metabolic-associated fatty liver disease (MAFLD) in combination with type 2 diabetes mellitus (T2DM) and small intestinal bacterial overgrowth (SIBO) syndrome. Materials and methods. The prospective, interventional, randomized study included 51 patients with MAFLD in combination with T2DM, who were examined and divided into 2 groups. Group 1 consisted of 24 patients with MAFLD and T2DM without SIBO. Group 2 was comprised of 27 patients with MAFLD in combination with T2DM and SIBO. The control group included 20 apparently healthy individuals. Serum levels of L-FABP and I-FABP were measured by ELISA method using the Human L-FABP and I-FABP ELISA Kit test systems, respectively (Elabscience, USA). Fecal numbers of B and F were determined by real-time PCR. Bacterial DNA was detected in a thermal cycler Rotor-Gene 6000 (QIAGEN, Germany) using DNA 16S rRNA primers and NanoDrop ND-8000 reagents (Thermo Scientific, USA). Results. To assess the state of intestinal permeability, serum levels of L-FABP and I-FABP were examined and numbers of phylum F and B as well as their ratio were calculated. Patients of both groups have been found to have increased serum levels of L-FABP, I-FABP, numbers of B in fecal samples and decreased numbers of F and F/B ratio. Conclusions. The study results obtained have revealed increased intestinal permeability and demonstrated an important diagnostic value of serum L-FABP and I-FABP as a biomarker of intestinal permeability in diabetic MAFLD patients with or without SIBO. Increased fecal numbers of Bacteroidetes, decreased numbers of Firmicutes and F/B ratio have been detected in diabetic MAFLD patients with or without SIBO. [ABSTRACT FROM AUTHOR]

Resveratrol butyrate ester (RBE), synthesized via the esterification of resveratrol and butyric acid, demonstrates better bioactivity than resveratrol. Therefore, we evaluated the anti-obesity effects of two RBE monomers with different numbers of ester, mono-ester derivative (3-O-butanoylresveratrol, ED4) and di-ester derivative (3,4′-di-O-butanoylresveratrol, ED2) in obese rats. Animals were assigned to the control diet, high-fat diet (HFD), HFD with ED4 (HFDM), and HFD with ED2 (HFDD) groups. After 6 weeks of treatment, the groups treated with ED4 and ED2 effectively regulated their basic biochemical indicators, including body weight and lipid parameters in serum and liver. Moreover, supplementation with ED4 and ED2 decreased the ratio of Firmicutes to Bacteroidetes and altered the levels of short-chain fatty acids, which may contribute to the anti-obesity effects. This research showcases the potential of RBE monomers in obesity prevention, particularly highlighting the greater efficacy of mono-ester RBE (ED4) compared to its di-ester form (ED2).

Background and Objectives: TB infection is one of the most challengeable epidemiological issues. Complex interactions between microbiota and TB infection have been demonstrated. Alteration in microbial population during TB infection may act as a useful biomarker. The present study examined the microbiota patterns of blood and sputum samples collected from Afghan immigrants and Iranian patients with active TB. Materials and Methods: Sixty active pulmonary TB patients were enrolled in the study. Blood and sputum samples were collected. To detect phylum bacterial composition in the blood and sputum samples, bacterial 16S rRNA quantification by Real-Time qPCR was performed. Results: A significant decrease in Bacteroidetes in Iranian sputum and blood samples of Afghan immigrants and Iranian TB active subjects were seen. While, sputum samples of Afghan immigrants showed no significant differences in Bacteroidetes abundance among TB active and control. Firmicutes were also presented no significant difference between sputum samples of the two races. Actinobacteria showed a significant increase in Iranian and Afghan sputum samples while this phylum showed no significant abundance in Iranian and Afghan TB positive blood samples. Proteobacteria also showed an increase in sputum and blood samples of the two races. Conclusion: An imbalance in Bacteroidetes and Firmicutes abundance may cause an alteration in the microbiota composition, resulting in dysregulated immune responses and resulting in the augmentation of opportunistic pathogens during TB infection, notably Proteobacteria and Actinobacteria. Evaluation of human microbiota under different conditions of TB infection can be critical to a deeper understanding of the disease control.

Abstract Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2–3 μm). The community from early March was typical for this season, with Alpha‐ and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Toward summer, Bacteroidetes, and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB‐dependent transporters of iron‐siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. This cheating ability of the Bacteroidetes may have contributed to their dominance in the summer.

Background/Objectives: The phyla Firmicutes and Bacteroidetes are the main constituents of the gut microbiota. An imbalance in the gut microbiota is a sign of dysbiosis, and the Firmicutes-to-Bacteroidetes ratio has been proposed to be a marker of it, especially in the context of obesity. Since Croatia is the country with one of the highest obesity rates in Europe, a pilot observational study was conducted. The aim of the study was to investigate the validity of this potential biomarker in a methodological study using sample processing, DNA sequence analysis and characterization of recruited participants, including various health factors. Methods: A study involving Croatian population was conducted. Participants age, body weight, gender, health history and lifestyle factors were recorded. Gut microbiota composition was analyzed using 16S rRNA sequencing. The F/B ratio was calculated and evaluated in the context of health factors. Statistical analysis was performed to detect the possible association of F/B ratio and excess body weight (kg) and possible impact of certain lifestyle factors. Results: No association between the F/B ratio and excess body weight (kg) was found. Excess body weight was significantly associated with higher age, male gender, and history of appendectomy. No significant health predictors of the F/B ratio were found, but weight gain was positively associated with a higher average F/B ratio. Conclusions: Although this study could not confirm the predictive value of the F/B ratio or any other phyla-related biomarker for excess body weight in the study population, it demonstrated interesting insights into the obesity-associated gut microbiota.

Obtaining body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well-documented that host-associated microorganisms play a vital role in animal physiology and behavior. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity, particularly the phyla Firmicutes and Bacteroidetes. The focus of most microbiome studies has been on human health or involved lab-reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we tested whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes were associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by analyzing 207 fecal samples collected over 5 summer active seasons. Results showed that marmots with higher mass gain rates had a greater relative abundance of Firmicutes. In contrast, a higher relative abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates in harsher environments. Although correlative, these results highlight the potential importance of symbiotic gut microbiota to mass gain in the wild—a trait associated with survival and fitness in many taxonomic groups. [ABSTRACT FROM AUTHOR]

Butyrate-producing bacteria are a functionally important part of the intestinal tract flora, and the resulting butyric acid is essential for maintaining host intestinal health, regulating the immune system, and influencing energy metabolism. However, butyrate-producing bacteria have not been defined as a coherent phylogenetic group. They are primarily identified using primers for key genes in the butyrate-producing pathway, and their use has been limited to the Bacillota and Bacteroidetes phyla. To overcome this limitation, we developed functional gene primers able to identify butyrate-producing bacteria through the butyrate kinase gene, which encodes the enzyme involved in the final step of the butyrate-producing pathway. Genomes extracted from human and rat feces were used to amplify the target genes through PCR. The obtained sequences were analyzed using BLASTX to construct a developmental tree using the MEGA software. The newly designed butyrate kinase gene primers allowed to recognize a wider diversity of butyrate-producing bacteria than that recognized using currently available primers. Specifically, butyrate-producing bacteria from the Synergistota and Spirochaetota phyla were identified for the first time using these primers. Thus, the developed primers provide a more accurate method for researchers and doctors to identify potential butyrate-producing bacteria and deepen our understanding of butyrate-producing bacterial species. [ABSTRACT FROM AUTHOR]

Context and aims. DNA metabarcoding strategy was used to sequence the 16S rRNA region of ruminal fluid samples from Nellore cattle fed with concentrate-rich diets in response to modulatory effect of buffering additives calcarea seaweed (Lithothamnium calcareum) and sodium bicarbonate. Methods. Besides characterising the richness and diversity indices of rumen bacterial community, the impact of potentially acidogenic diets on rumen pH, blood parameters, and short-chain fatty acid profile (SCFA) was investigated for which four male Nellore cattle were used, distributed in a 4 × 4 Latin square (treatments × periods). Treatments comprised the same highly concentrated basal diet, and were as follows: T1, without additive (CON); T2, inclusion of 90 g of sodium bicarbonate (BIC); T3, inclusion of 90 g of L. calcareum (L90); and T4, inclusion of 45 g of L. calcareum (L45). Data were analysed in R, in which diversity and abundance at gender level were analysed using Friedman's test, withmeans being adjusted by False Discovery Rate (FDR) correction. The analyses of pH, biochemical parameters and SCFA were analysed using Scott-Knott test and means were evaluated with a significance level of 10% (P < 0.10). Key results. We identified 1474 operational taxonomic units (OTUs) belonging to 52 genera and 16 phyla of bacteria domain. The results showed that bacterial microbiota were dominated by Firmicutes (44.12%), Bacteroidetes (28.29%), and Proteobacteria (5.88%). Animals fed with L90 demonstrated greater abundance and ruminal diversity for the Prevotella genus (P < 0.07% and P < 0.09% respectively), whereas cattle supplemented with L45 demonstrated greater diversity of the Fibrobacter genus (P < 0.05). There were differences in molar proportion for acetic (P < 0.07%) and valeric (P < 0.03%) acids in the period before feeding. Higher blood lactate concentrations were observed in animals supplemented with L45 (P < 0.06%), while animals that received treatments L90 and BIC presented lower levels of blood lactate. This metabolite was lower in animals fed with 90 g of sodiumbicarbonate and L. calcareum daily. These treatments also reduced the concentration of acetic acid and increased that of valeric acid, and improved ruminal diversity. Conclusions and implications. Our results supported this choice to improve ruminal function, with a great prospective of better weight-gain performance in Nellore cattle. [ABSTRACT FROM AUTHOR]

Catabolism of algal polysaccharides by marine bacteria is a significant process of marine carbon cycling. β1,3/1,4-Mixed-linkage xylan (MLX) is a class of xylan in the ocean, widely present in the cell walls of red algae. However, the catabolic mechanism of MLX by marine bacteria remains elusive. Recently, we found that a marine Bacteroidetes strain, Polaribacter sp. Q13, is a specialist in degrading MLX, which secretes a novel MLX-specific xylanase. Here, the catabolic specialization of strain Q13 to MLX was studied by multiomics and biochemical analyses. Strain Q13 catabolizes MLX with a canonical starch utilization system (Sus), which is encoded by a single xylan utilization locus, XUL-Q13. In this system, the cell surface glycan-binding protein SGBP-B captures MLX specifically, contributing to the catabolic specificity. The xylanolytic enzyme system of strain Q13 is unique, and the enzymatic cascade dedicates the stepwise hydrolysis of the β1,3- and β1,4-linkages in MLX in the extracellular, periplasmic, and cytoplasmic spaces. Bioinformatics analysis and growth observation suggest that other marine Bacteroidetes strains harboring homologous MLX utilization loci also preferentially utilize MLX. These results reveal the catabolic specialization of MLX degradation by marine Bacteroidetes, leading to a better understanding of the degradation and recycling of MLX driven by marine bacteria. [ABSTRACT FROM AUTHOR]

Background: Heat shock proteins (HSP) protect cancer cells. Gastrointestinal bacteria contain HSP genes and can release extracellular vesicles which act as biological shuttles. Stress from treatment may result in a microbial community with more HSP genes, which could contribute to circulating HSP levels. Methods: The authors examined the abundance of five bacterial HSP genes pre-treatment and during induction in stool sequences from 30 pediatric acute lymphoblastic leukemia patients. Results: Decreased mean HTPG counts (p = 0.0024) pre-treatment versus induction were observed. During induction, HTPG, Shannon diversity and Bacteroidetes decreased (p = 7.5e-4; 1.1e–3; 8.6e-4), while DNAK and Firmicutes increased (p = 6.9e-3; 9.2e-4). Conclusion: Understanding microbial HSP gene community changes with treatment is the first step in determining if bacterial HSPs are important to the tumor microenvironment and leukemia treatment. [ABSTRACT FROM AUTHOR]

Introduction: The gut microbiota closely relates to host health, whereas the relationship between gut microbiota and testosterone during the development of Meishan male pigs remains unclear. This study investigated the fecal microbiota composition and testosterone level during development in Meishan male pigs. Methods: Fresh fecal samples of 20 healthy Meishan male pigs were individually collected at 10 and 22 weeks (wk) of age for testosterone content detection and bacteria pyrosequencing analysis. Anaerobic culture experiment of fecal bacteria in vitro was performed for bacteria pyrosequencing analysis. Results: The fecal testosterone content increased significantly from 10 weeks (wk) to 22 wk of age (P < 0.05). Meanwhile, the boars at 22 wk had a lower abundance of phylum Bacteroidetes and Proteobacteria, and genus Alloprevotella, Prevotella_1, Prevotellaceae_NK3B31_group, and Streptococcus in the fecal microbiota composition (P < 0.05). but higher proportions of the phylum Actinobacteria, Firmicutes, Kiritimatiellaeota, and Tenericutes, and genus Clostridium_sensu_ stricto_1, Muribaculaceae and Terrisporobacter than that at 10 wk (P < 0.05), and the Firmicutes to Bacteroidetes ratio was higher at 22 wk than 10 wk (P < 0.05). Moreover, the fecal testosterone level significantly correlated with the relative abundance of the phylum Actinobacteria, Firmicutes, and Tencuteseri, and genus Alloprevotella, Clostridium_sensu_stricto_1, Muribaculaceae, Prevotella_1 and Streptococcus. Furthermore, the in vitro experiments indicated that the abundance of the phylum Proteobacteria and genus Escherichia-Shigella reduced with the increase of supplemental testosterone level. In contrast, the proportion of Firmicutes phylum increased with additional testosterone levels. Discussion: Testosterone could modulate the microflora structure. Meanwhile, the bacteria could degrade the testosterone in a dose testosterone-dependent manner. These results provide us with new insights into the relationship between the gut microbiome and testosterone and the contributions of the gut microbiome in physiological regulation in response to gonad development. [ABSTRACT FROM AUTHOR]

The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15–37 °C (optimally at 28 °C), at pH 6.0–8.5 (optimally at pH 7.0) and in the presence of 1–5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T). [ABSTRACT FROM AUTHOR]

Abstract Background Epilepsy is a chronic neurological condition that disrupts the normal functioning of the brain and it is characterized by seizures. Research suggests the involvement of the Gut-Brain axis in epilepsy. This study seeks to determine the role of the gut microbiota in the anticonvulsant effect of basil oil (BO) using antibiotic-depleted and altered germ-free mice against naïve mice in Pentylenetetrazole (PTZ) induced seizure model. There is an ever growing interest in improvement of treatment outcomes in epilepsy and also in the development of newer therapeutic options, especially in the population of patients that do not attain seizure relief from available antiseizure medications (ASMs). According to research, gut microbiota can alter brain function and development. Increasing evidence suggests disrupting the delicate symbiotic balance existing between the gut and brain results in disease conditions. Also, the oil from Ocimum basilicum L., (BO) has been proven scientifically to significantly block clonic seizures induced by PTZ and picrotoxin in seizure models. Methods The microbiota of mice were depleted or altered by administering cocktail antibiotics and individual antibiotics respectively. DNA was isolated from mouse stool, and then the 16S ribosomal ribonucleic acid (16S rRNA) gene was quantitatively amplified using reverse transcription-polymerase chain reaction (RT-PCR). Amplicons were sequenced to determine the phylogenetic make-up of the bacteria involved. Metabolic profiles of the serum and stool of mice were determined using Proton (1H) Nuclear Magnetic Resonance (NMR) spectroscopy. Results Cocktail antibiotic pre-treatment significantly reversed the anticonvulsant effect of BO by increasing frequency and duration of seizures but did not affect latency to seizure. In mice pre-treated with single antibiotics, the anticonvulsant effect of BO was lost as latency to seizures, frequency and duration of seizures increased compared to mice that received only BO. Assessment of the phylogenetic make-up of the microbiota in antibiotic pre-treated mice showed a distorted composition of the microbiota compared to the control group. Conclusion Depletion of the microbiota significantly reversed the anticonvulsant actions of BO. The concentrations of short chain fatty acids (SCFAs) was higher in stool than in the serum of the mice. Administration of BO probably does not influence the microbial composition within the mouse microbiota. The elevated ratio of Firmicutes to Bacteroidetes in microbiota-depleted groups might have contributed to the reversal of anticonvulsant actions of BO.

This study aimed to investigate the immediate and continual perturbation to the gut microbiota of offspring in the weeks post-weaning and how these may be modulated by treating pregnant C57BL/6J dams with antibiotics (ABX). We used a broad-spectrum antibiotic cocktail consisting of ampicillin 1 mg/mL, neomycin 1 mg/mL, and vancomycin 0.5 mg/mL, or vancomycin 0.5 mg/mL alone, administered ad-lib orally to dams via drinking water during gestation and stopped after delivery. We analyzed the gut microbiota of offspring, cytokine profiles in circulation, and the brain to determine if there was evidence of a gut-immune-brain connection. Computationally predicted metabolic pathways were calculated from 16s rRNA sequencing data. ABX treatment can negatively affect the gut microbiota, including reduced diversity, altered metabolic activity, and immune function. We show that the maternal ABX-treatment continues to alter the offspring's gut microbiota diversity, composition, and metabolic pathways after weaning, with the most significant differences evident in 5-week-olds as opposed to 4-week-olds. Lower levels of chemokines and inflammatory cytokines, such as interleukin (IL)-1α and IL-2, are also seen in the periphery and brains of offspring, respectively. In conclusion, this study shows maternal antibiotic administration alters gut microbiome profiles in offspring, which undergoes a continuous transformation, from week to week, at an early age after weaning.

The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes beneficial for their host's self-defense (e.g., antibiotic resistance) or ability to compete for essential or limited resources (e.g., vitamins). Vitamin B12 and related compounds (corrinoids) are critical nutrients that enable colonization by members of the common gut microbe phylum, the Bacteroidetes. Herein, we identify a distinct class of MGEs in the Bacteroidetes responsible for the mobilization and exchange of the genes required for transport of corrinoids, a group of cyclic tetrapyrrole cofactors including vitamin B12 (btuGBFCD). This class includes two distinct groups of conjugative transposons (CTns) and one group of phage. Conjugative transfer and vitamin B12 transport activity of two of the CTns were confirmed in vitro and in vivo, demonstrating the important role MGEs play in distribution of corrinoid transporters in the Bacteroidetes.