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Metabolic disorders present a significant public health challenge globally. The intricate relationship between the gut microbiome, particularly Bacteroides spp. (BAC), and obesity, including their specific metabolic functions, remains partly unresolved. This review consolidates current research on BAC's role in obesity and lipid metabolism, with three objectives: (1) To summarize the gut microbiota's impact on obesity; (2) To assess BAC's efficacy in obesity intervention; (3) To explore BAC's mechanisms in obesity and lipid metabolism management. This review critically examines the role of BAC in obesity, integrating findings from clinical and preclinical studies. We highlight the changes in BAC diversity and concentration following successful obesity treatment and discuss the notable differences in BAC characteristics among individuals with varying obesity levels. Furthermore, we review recent preclinical studies demonstrating the potential of BAC in ameliorating obesity and related inflammatory conditions, providing detailed insights into the methodologies of these in vivo experiments. Additionally, certain BAC-derived metabolites have been shown to be involved in the regulation of host lipid metabolism-related pathways. The enhanced TNF production by dendritic cells following BAC administration, in response to LPS, also positions BAC as a potential adjunctive therapy in obesity management. [ABSTRACT FROM AUTHOR]

Bacteroides spp. are prominent members of the human gut microbiota that play critical roles in the metabolism of complex carbohydrates from the daily diet. Hyaluronic acid (HA) is a multifunctional polysaccharide which has been extensively used in the food and biomedical industry. However, how HA is degraded and fermented by Bacteroides spp. has not been fully characterized. Here, we comprehensively investigated the detailed degradation profiles and fermentation characteristics of four different HAs with discrete molecular weight (Mw) by fourteen distinctive Bacteroides spp. from the human gut microbiota. Our results indicated that high-Mw HAs were more degradable and fermentable than low-Mw HAs. Interestingly, B. salyersiae showed the best degrading capability for both high-Mw and low-Mw HAs, making it a keystone species for HA degradation among Bacteroides spp.. Specifically, HA degradation by B. salyersiae produced significant amounts of unsaturated tetrasaccharide (udp4). Co-culture experiments indicated that the produced udp4 could be further fermented and utilized by non-proficient HA-degraders, suggesting a possible cross-feeding interaction in the utilization of HA within the Bacteroides spp.. Altogether, our study provides novel insights into the metabolism of HA by the human gut microbiota, which has considerable implications for the development of new HA-based nutraceuticals and medicines. [ABSTRACT FROM AUTHOR]

The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes. [ABSTRACT FROM AUTHOR]

Abstract: Bacteroides spp. represent a prominent bacterial group in human intestinal microbiota with roles in symbiosis and pathogenicity; however, the detailed composition of this group in human feces has yet to be comprehensively characterized. In this study, the molecular diversity of Bacteroides spp. in human fecal microbiota was analyzed from a seven-member, four-generation Chinese family using Bacteroides spp. group-specific 16S rRNA gene clone library analysis. A total of 549 partial 16S rRNA sequences amplified by Bacteroides spp.-specific primers were classified into 52 operational taxonomic units (OTUs) with a 99% sequence identity cut-off. Twenty-three OTUs, representing 83% of all clones, were related to 11 validly described Bacteroides species, dominated by Bacteroides coprocola, B. uniformis, and B. vulgatus. Most of the OTUs did not correspond to known species and represented hitherto uncharacterized bacteria. Relative to 16S rRNA gene universal libraries, the diversity of Bacteroides spp. detected by the group-specific libraries was much higher than previously described. Remarkable inter-individual differences were also observed in the composition of Bacteroides spp. in this family cohort. The comprehensive observation of molecular diversity of Bacteroides spp. provides new insights into potential contributions of various species in this group to human health and disease. [Copyright &y& Elsevier]

Abstract Probiotics play important roles on sustaining or reconstructing the homeostasis of intestinal microbiota, which is one of the key factors in alleviating diseases and maintaining the healthy condition of the host. Preclinical trials indicate that Bacteroides genus is widely considered as source of novel beneficial candidates for attenuating inflammation by regulating lymphocytes and cytokine expression, controlling metabolism and preventing cancer. Furthermore, the first case of authorization of Bacteroides xylanisolvens in food by the European Commission opens the gate for further investigation and application of this promising community. With this paper, we summarized current investigations of discovering beneficial Bacteroides strains, exploring their interaction mechanisms with the host, and evaluating the potential safety risks during commercialization. Graphical abstract Unlabelled Image Highlights • Bacteroides spp. interact with the host by modifying immune cells and regulating metabolites. • Bacteroides spp. can improve different intestinal disorders, as well as cardiovascular disease, behavior disorders and cancer. • Bacteroides strains have been started in authorization in food processing by the European Commission after safety evaluation. • Bacteroides genus is widely considered as source of next-generation probiotics. [ABSTRACT FROM AUTHOR]

Achyranthes bidentata (A. bidentata) is a famous traditional Chinese medicine (TGM) for treatment osteoporosis. Polysaccharides, a major factor for shaping the gut microbiota, are the primary ingredients of A. bidentata. However, bioactivity of A. bidentata polysaccharide on human gut microbiota (HGM) remains unknown. Here, a homogeneous pectic polysaccharide A23–1 with average molecular weight of 93.085 kDa was extracted and purified from A. bidentata. And A23–1 was compsed of rhamnose, glucuronic acid, galacturonic acid, glucose, galactose and arabinose in a molar ratio of 7.26: 0.76: 5.12: 2.54: 23.51: 60.81. GC–MS, partial acid hydrolysis and NMR results indicated the backbone of A23–1 was composed of 1, 2, 4-Rha p and 1, 4-Gla p A, while the branches were composed of galactose, arabinose, glucose and glucuronic acid. Further, A23–1 was found to be degraded into monosaccharides and fragments. Taking Bacteroides thetaiotaomicron (BT) as a model, we suggested three polysaccharide utilization loci (PULs) might be involved in the A23–1 degradation. Degraded products generated by BO might not support the growth of probiotics. Besides, acetate and propionate as the main end products were generated by Bacteroides spp. and probiotics utilizing A23–1. These findings suggested A23–1 was possible one of food sources of human gut Bacteroides spp. • The structure of a pectic polysaccharide A23–1 from A. bidentata was elucidated. • A23–1 could be degraded by human gut Bacteroides spp. • The degradation process might be dictated by three PULs. • There was possible no cross feeding between Bacteroides ovatus and probiotics. • Bacteroides spp. produced SCFAs by utilizing A23–1. [ABSTRACT FROM AUTHOR]

Bacteroides spp. are members of the human gut microbiota that confer myriad benefits on their hosts. Among them is the provision of energy from otherwise indigestible polysaccharides comprising part of the host diet, lining the intestinal mucosal layer, and decorating the surface of other microbes. Bacteroides spp. devote ∼20% of their genomes to the transport and breakdown of a wide variety of polysaccharides, and to the regulation of these processes. Bacteroides spp. rely on different families of transcriptional regulators to ensure that carbohydrate utilization genes are expressed under specific conditions. The regulators and mechanisms controlling carbohydrate utilization are often unique to these gut-dwelling bacteria, and do not conform to those of model organisms. [ABSTRACT FROM AUTHOR]

An experimental group of one-day-old chicken from a commercial hatchery was given a defined mixture of 7 gut anaerobes. The next day the chicks were inoculated by an APEC strain O78:H4-ST117 resistant to ciprofloxacin, alongside with the control group and monitored for 4 wk after the inoculation for the presence of the colonizing strains and ciprofloxacin-resistant E. coli. Significant reduction of colonization rates in the first 2 wk was recorded in the experimental group for the numbers of ciprofloxacin-resistant E. coli. The results show that colonization of chicken by defined anaerobic mixtures may provide a decisive protection during the critical period of the chicken intestinal microflora development. [ABSTRACT FROM AUTHOR]

Inflammatory alteration of the feature of gut microbiota is one of causative factors for depressive disorders. Here, we examined whether ingestion of magnesium-rich (212 ppm) mineral hard water (mineral water), which prevents gut inflammation, had prophylactic effect on development of depressive-like phenotypes in 10-days social defeat stress (SDS)-subjected C57BL/6J mice. SDS-susceptible mice with social disability exhibited increased body weight gain, and ingestion of mineral water ameliorated the increased body weight gain without any effects on daily food consumption or water intake. Relative abundance of Bacteroides spp. in colonic microbiota was decreased in water- and mineral water-ingesting SDS-susceptible mice, the level of reduction in the former being greater than in the latter, and was correlated inversely with body weight gain, and positively with sociability of mice. Overall, it is suggested that ad libitum magnesium-rich mineral water ingestion ameliorates development of psychosocial stress-induced depressive-like phenotypes partially via preventing decrease of colonic Bacteroides spp. [ABSTRACT FROM AUTHOR]

Gut microbiota are significantly associated with the occurrence and development of inflammatory bowel disease (IBD). Panax notoginseng saponins (PNS) could be used for colitis and to modulate gut microbiota. However, the mechanism behind the effects of PNS on anti-colitis that are pertinent to gut microbiota is largely unknown. This study aimed to evaluate the anti-colitis effects of PNS and explore the involved mechanism as it is related to gut microbiota. Results showed that PNS significantly alleviated dextran sulfate sodium (DSS)-induced colitis. Meanwhile, after PNS treatment, the tight junction proteins were enhanced and proinflammatory cytokines, such as TNF- α , IL-6, IL-1 β , and IL-17, were decreased. Furthermore, Bacteroides spp. were significantly increased after modeling, while PNS reduced their abundance and significantly increased the amount of Akkermansia spp. in vivo. Importantly, Akkermansia spp. and Bacteroides spp. were correlated with the IBD disease indicators. Moreover, fecal microbiota transplantation (FMT) experiments confirmed that PNS-reshaped gut microbiota significantly alleviated DSS-induced colitis, while A. muciniphila significantly reduced the levels of the LPS-induced cellular inflammatory factors IL-1 β and TNF- α. In conclusion, PNS alleviated colitis pertinent to the upregulation of Akkermania spp. and downregulation of Bacteroides spp. in the gut. [ABSTRACT FROM AUTHOR]

Ethanol extracts obtained from 13 poplar propolis samples originating from various European countries by traditional maceration were tested for total polyphenols, flavonoid content, and antioxidant activity. Moreover, the content of 18 polyphenolic compounds (from the group of phenolic acids and flavonoids) was determined using the HPLC method. The inhibitory effect of six selected extracts with the highest activity was assessed by well-diffusion method against five strains (Bifidobacterium spp., L. rhamnosus, L. acidophilus, E. coli, and Bacteroides spp.) of intestinal bacteria self-isolated from the faeces of obese probands with the use of selective media. It was found that the antioxidant activity of propolis varied depending on geographical origin and even among samples from the same region, which indicates that some other factors also influence propolis quality. The samples of different geographical origin varied mainly in the share of individual phenolic compounds, and it was not possible to find a characteristic marker of origin, excluding the galangin present in the Polish samples only. Assessing the inhibitory activity of propolis (in the range of 70 mg to 10 µg per mL) indicated that the concentration of 100 µg/mL was found as being safe for tested fecal bacteria (Bifidobacterium spp., L. rhamnosus, L. acidophilus, E. coli, and Bacteroides spp.). As no negative effect of low doses of propolis on the intestinal microflora was found, it can be suggested that its use in recommended doses brings only beneficial effects to the body. [ABSTRACT FROM AUTHOR]

Severe COVID-19 and MIS-C are rare but serious outcomes associated with SARS-CoV-2 infection. The onset of MIS-C often involves the gastrointestinal system, suggesting a potential connection with gut microbiota. This study aims to compare the gut microbiota of children with severe COVID-19 and those with MIS-C using various biomolecular approaches. Gut microbiota composition and specific microbial modulations were analyzed using fecal samples collected at hospital admission. The study included hospitalized patients (mean age 6 ± 5 years) diagnosed with severe COVID-19 (37 patients) or MIS-C (37 patients). Microbial differences were assessed using both NGS and qRT-PCR methodologies. In 75% of cases, pharmacological treatments included antibiotics and corticosteroids, which influenced the microbiota composition. Early age was found to have the most significant impact on microbiota diversity. Significant differences in alpha and beta diversity were observed between COVID-19 and MIS-C patients, particularly concerning low-abundance species. Levels of Bacteroides spp., Bifidobacterium spp., and Akkermansia muciniphila were comparable between groups, while an increased activity of Bifidobacterium spp. was noted in children with positive fecal samples (p = 0.019). An in-depth evaluation of lesser-known gut species may be key to reducing the risk of severe outcomes and developing microbiota-based biomarkers for the early diagnosis of MIS-C. [ABSTRACT FROM AUTHOR]

Pathogenic changes in gut microbial composition precede the onset of HIV-1 infection in men who have sex with men (MSM). This process is associated with increased levels of systemic inflammatory biomarkers and risk for AIDS development. Using mediation analysis framework, in this report we link the effects of unprotected receptive intercourse among MSM prior to primary HIV-1 infection to higher levels of proinflammatory cytokines sCD14 and sCD163 in plasma and a significant decrease in the abundance of A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp., and a potential increase in the abundance of Dehalobacterium spp. and Methanobrevibacter spp. in stools of MSM with the highest number of sexual partners. These differences in microbiota, together with a reduction in the pairwise correlations among commensal and short-chain fatty acid-producing bacteria with a number of sexual partners, support an increase in gut dysbiosis with the number of sexual partners. These results demonstrate the interconnectedness of sexual behavior, immune response, and microbiota composition, notably among MSM participating in high-risk sexual behaviors. Sexual behavior among men who have receptive anal intercourse with men is linked to changes in the gut microbiome and systemic inflammation leading to HIV-1 infection. [ABSTRACT FROM AUTHOR]

Sanfilippo syndrome, or mucopolysaccharidosis type III (MPS III), is a rare lysosomal disease caused by congenital enzymatic deficiencies in heparan sulfate (HS) degradation, leading to organ dysfunction. The most severe hallmark of MPS III comprises neurological alterations, although gastrointestinal symptoms (GISs) have also been shown to be relevant in many patients. Here, we explored the contribution of the gut microbiota to MPS III GISs. We analyzed the composition and functionality of the gut microbiota in two MPS III siblings with the same mutation (c.544C > T, c.1080delC, in the SGSH gene) and the same diet, but with differences in their GISs, including recurrent diarrhea in one of them. Using 16S sequencing, we observed that the MPS III patients exhibited decreased alpha diversity and a lower abundance of Lachnospiraceae and Bifidobacteriaceae accompanied by a higher abundance of the Ruminococcaceae and Rikenellaceae families than the healthy control subjects. Comparing siblings, we found an increased abundance of Bacteroidaceae and a lower abundance of Ruminococcaceae and Akkermansiaceae in the GIS-free patient. This patient also had a higher relative abundance of Sus genes (SusA, SusB, SusE, and SusG) involved in glycosaminoglycan metabolism. We found higher HS levels in the stool of the two MPS III patients than in healthy volunteers, particularly in the patient with GISs. Functionally, whole fecal metabolites from the patient with GISs induced oxidative stress in vitro in healthy monocytes. Finally, the Bacteroides thetaiotaomicron strain isolated from MPS III stool samples exhibited HS degradation ability. Overall, our results reveal different microbiota compositions and functionalities in MPS III siblings, who exhibited differential gastrointestinal symptomatology. Our study may serve as a gateway to explore the impact of the gut microbiota and its potential to enhance the quality of life in Sanfilippo syndrome patients. [ABSTRACT FROM AUTHOR]

The aim: to find connections between gut microbiota composition and transthoracic echocardiography (TTE) indexes in patients with coronary artery disease (CAD) and atrial fibrillation (AF). Materials and methods: 300 patients were divided into 3 groups: first (CAD) – 149 patients with CAD but without arrhythmias; second (CAD+AF) – 124 patients with CAD and AF paroxysm; and the control group – 27 patients without CAD and arrhythmias. 16-S rRNA sequencing checked gut microbiota composition. TTE was done by ALOKA SSD-5000. Results: The II group patients were characterized by the increase of LAD (10.03 %), LAV (15.40 %) and LAVI (11.48 %) in comparison with the I group, P<0.05. The II group patients were characterized by a rise of Pseudomonadota in comparison with the I group, P<0.05. Also, II group patients were characterized by rise of Actinobacter Spp. and decrease of Blautia Spp., Bacteroides Thetaiotaomicron in comparison with the I group, P<0.05. Firmicutes were correlated with AO (r=0.308), LADI (r=-0.363), RV (r=-0.470), IVS (r=-0.381), LVPW (r=-0.345), LVM (r=-0.476) and EF (r=0,312), P<0.05. Akkermansia Muciniphila was correlated with LAD (r=-0.343), LADI (r=-0.308), LAV (r=-0.494), LAVI (r=-0.488), RAV (r=-0.316), RAVI (r=-0.397), RV (r=-0.383), EF (r=0.332), P<0.05. Bifidobacterium Spp. were correlated with LAV (r=-0.487), LAVI (r=-0.327), RV (r=-0.341), IVS (r=-0.306), RWT (r=-0.389), LVM (r=-0.369), LVMI (r=-0.312), EF (r=0.317), P<0.05. Streptococcus Spp. were correlated with AO (r=0,329), LVOT (r=0,390), RV (r=0,393), IVS (r=0,648), LVPW (r=0,579), RWT (r=0,356), LVM (r=0,336), LVMI (r=0,376), P<0.05. Ruminococcus Spp. were correlated with AO (r=0,412), LVOT (r=0,351), LADI (r=-0.343), IVS (r=-0.316), LVPW (r=-0.367), LVM (r=-0.302), LVMI (r=-0.379), P<0.05. Conclusion: Gut microbiota composition and TTE indexes play a significant role in CAD and AF pathogenesis. Firmicutes, Bifidobacterium spp., and Verrucomicrobiota (Akkermansia muciniphila) were significantly correlated with left atrium size and volume, as well as their ultrasound indexes. Bifidobacterium spp., Bacteroides Spp., Streptococcus Spp. and Ruminococcus Spp. were significantly correlated with left ventricular sizes and its hypertrophy indexes. [ABSTRACT FROM AUTHOR]

Owing to the well-established application of prebiotics in human food products, there is a growing interest in their potential as dietary supplements for gut microbiota composition and improvement of the digestive health of dogs. However, targeted studies with dogs as research subjects are still limited. In the present study, an in vitro simulated gut microbiota fermentation system using canine feces from a healthy Border Collie breed was used to investigate the prebiotic effects of five different oligosaccharides and compare their regulatory effects on the gut microbiota structure and the resultant metabolites. Due to the addition of oligosaccharides, the fermented samples had lower pH and higher bacterial proliferation. The oligosaccharide-fermentation selectively boosted Lactobacillus spp., Streptococcus spp., Enterococcus spp., Bacteroides spp., and hindered Escherichia-Shigella spp., Paeniclostridium, spp., and Bacteroides spp. Each oligosaccharide showed distinct characteristics and preferences for regulating gut microbiota structure and abundance. Furthermore, the addition of oligosaccharides increased the production of short-chain fatty acids, particularly butyric acid. This study provides a preliminary basis for the rapid and rational selection of prebiotic oligosaccharides as canine dietary supplements and further explores the function of oligosaccharides and their combinations in canine health. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Specific human gut microbes inhabit the outer mucus layer of the gastrointestinal tract. Certain residents of this niche can degrade the large and complex mucin glycoproteins that constitute this layer and utilise the degradation products for their metabolism. In turn, this microbial mucin degradation drives specific microbiological ecological interactions in the human gut mucus layer. However, the exact nature of these interactions remains unknown. In this study, we designed and studied an in vitro mucin-degrading synthetic community that included mucin O-glycan degraders and cross-feeding microorganisms by monitoring community composition and dynamics through a combination of 16S rRNA gene amplicon sequencing and qPCR, mucin glycan degradation with PGC-LC–MS/MS, production of mucin-degrading enzymes and other proteins through metaproteomics, and metabolite production with HPLC. We demonstrated that specialist and generalist mucin O-glycan degraders stably co-exist and found evidence for cross-feeding relationships. Cross-feeding on the products of mucin degradation by other gut microbes resulted in butyrate production, hydrogenotrophic acetogenesis, sulfate reduction and methanogenesis. Metaproteomics analysis revealed that mucin glycan degraders Akkermansia muciniphila , Bacteroides spp. and Ruminococcus torques together contributed 92% of the total mucin O-glycan degrading enzyme pool of this community. Furthermore, comparative proteomics showed that in response to cultivation in a community compared to monoculture, mucin glycan degraders increased carbohydrate-active enzymes whereas we also found indications for niche differentiation. These results confirm the complexity of mucin-driven microbiological ecological interactions and the intricate role of carbohydrate-active enzymes in the human gut mucus layer. [ABSTRACT FROM AUTHOR]

Simple Summary: We report on the changes observed in the microbiomes of fifty-four dogs that received fecal transplants (FMTs) in the form of oral capsules for their chronic vomiting, diarrhea, and/or constipation. We found that the relative abundances of short-chain fatty acid producing bacteria increased after FMT. The microbiome compositions of dogs before and after FMT were associated with the diet and antibiotic history. Furthermore, we found that certain groups of donor bacteria were more commonly shared with the FMT recipient. Lastly, our data suggested that a high degree of overlap between the microbiome of the donor and that of the recipient was negatively associated with bacterial engraftment, and could be an important factor to consider when evaluating the impact of FMTs on the host and its microbiome. Fecal microbiota transplants (FMTs) have been successful at treating digestive and skin conditions in dogs. The degree to which the microbiome is impacted by FMT in a cohort of dogs has not been thoroughly investigated. Using 16S rRNA gene sequencing, we document the changes in the microbiome of fifty-four dogs that took capsules of lyophilized fecal material for their chronic diarrhea, vomiting, or constipation. We found that the relative abundances of five bacterial genera (Butyricicoccus, Faecalibacterium, Fusobacterium, Megamonas, and Sutterella) were higher after FMT than before FMT. Fecal microbiome alpha- and beta-diversity were correlated with kibble and raw food consumption, and prior antibiotic use. On average, 18% of the stool donor's bacterial amplicon sequence variants (ASVs) engrafted in the FMT recipient, with certain bacterial taxa like Bacteroides spp., Fusobacterium spp., and Lachnoclostridium spp. engrafting more frequently than others. Lastly, analyses indicated that the degree of overlap between the donor bacteria and the community of microbes already established in the FMT recipient likely impacts engraftment. Collectively, our work provides further insight into the microbiome and engraftment dynamics of dogs before and after taking oral FMTs. [ABSTRACT FROM AUTHOR]

Simple Summary: Conventional diversity metrics do not fully capture treatment impacts on microbial diversity. An innovative community modulation score (CMS), coupled with the predictive SIFR® technology, underlined the potential of a bacterial long-chain dextran as a booster of microbial diversity, as compared to the well-established prebiotic inulin. Long-chain dextrans are α-glucans that can be produced by lactic acid bacteria. NextDextTM, a specific long-chain dextran with a high degree of polymerisation, produced using Weissella cibaria, was recently shown to exert prebiotic potential in vitro. In this study, the ex vivo SIFR® technology, recently validated to provide predictive insights into gut microbiome modulation down to the species level, was used to investigate the effects of this long-chain dextran on the gut microbiota of six human adults that altogether covered different enterotypes. A novel community modulation score (CMS) was introduced based on the strength of quantitative 16S rRNA gene sequencing and the highly controlled ex vivo conditions. This CMS overcomes the limitations of traditional α-diversity indices and its application in the current study revealed that dextran is a potent booster of microbial diversity compared to the reference prebiotic inulin (IN). Long-chain dextran not only exerted bifidogenic effects but also consistently promoted Bacteroides spp., Parabacteroides distasonis and butyrate-producing species like Faecalibacterium prausnitzii and Anaerobutyricum hallii. Further, long-chain dextran treatment resulted in lower gas production compared to IN, suggesting that long-chain dextran could be better tolerated. The additional increase in Bacteroides for dextran compared to IN is likely related to the higher propionate:acetate ratio, attributing potential to long-chain dextran for improving metabolic health and weight management. Moreover, the stimulation of butyrate by dextran suggests its potential for improving gut barrier function and inflammation. Overall, this study provides a novel tool for assessing gut microbial diversity ex vivo and positions long-chain dextran as a substrate that has unique microbial diversity enhancing properties. [ABSTRACT FROM AUTHOR]

The ageing of an organism is associated with certain features of functional decline that can be assessed at the cellular level (e.g., reduced telomere length, loss of proteostasis, etc.), but also at the organismic level. Frailty is an independent syndrome that involves increased multidimensional age-related deficits, heightens vulnerability to stressors, and involves physical deficits in mainly the locomotor/muscular capacity, but also in physical appearance and cognition. For sporadic Alzheimer's disease, age per se is one of the most relevant risk factors, but frailty has also been associated with this disease. Therefore, we aimed to answer the two following questions within a cross-sectional study: (1) do Alzheimer's model mice show increased frailty, and (2) what changes of the microbiota occur concerning chronological age or frailty? Indeed, aged 5xFAD mice showed increased frailty compared to wild type littermates. In addition, 5xFAD mice had significantly lower quantities of Bacteroides spp. when only considering frailty, and lower levels of Bacteroidetes in terms of both frailty and chronological age compared to their wild type littermates. Thus, the quality of ageing—as assessed by frailty measures—should be taken into account to unravel potential changes in the gut microbial community in Alzheimer's disease. [ABSTRACT FROM AUTHOR]

Recently, many cases of mixed invasion by Giardia and ascarids have been registered. Gastrointestinal lesions in patients are often accompanied by dysbiotic changes. The aim was to study the effect of probiotics containing Saccharomyces bouvardias CNCM I-745 in the complex therapy of patients with giardiasis, ascariasis, and mixed invasion. 90 patients with giardiasis, ascariasis and mixed invasion were divided into 3 groups, depending on the type of invasion. Each group was divided into two subgroups, depending on the treatment (basic treatment and treatment with probiotics). When studying the state of the intestinal microbiota, the following changes were detected in all patients before treatment. The content of Bifidobacterium spp., Lactobacillus spp., Enterococcus spp. and the total content of E. coli was reduced. At the same time, there was an increase in the content of Peptostreptococcus spp., Bacteroides spp., E. coli with low enzymatic properties, hemolytic E. coli, opportunistic Enterobacteriaceae spp., Candida spp. and Staphylococcus spp. Under the influence of treatment, the subgroup with probiotics addition to the basic treatment, was more effective for all types of invasions. The use of probiotics containing Saccharomyces bouvardias CNCM I-745 in the complex therapy of patients with mixed invasion of giardiasis and ascariasis increased treatment efficiency following a significant improvement in intestinal microbiota. [ABSTRACT FROM AUTHOR]

Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis- and trans-encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research. [ABSTRACT FROM AUTHOR]

Biological aging is linked to altered body composition and reduced neuroactive steroid hormones like dehydroepiandrosterone sulfate (DHEAS), which can stimulate the GABA signaling pathway via gut microbiota. Our study examined the association of gut microbiota with lifespan in mice through comprehensive analysis of its composition and functional involvement in cholesterol sulfate, a precursor of DHEAS, metabolism. We used 16S rRNA and metagenomic sequencing, followed by metabolic pathway prediction and thin layer chromatography and MALDI-TOF cholesterol sulfate identification. Significant increases in bacteria such as Bacteroides , typical for long-lived and Odoribacter and Colidextribacter , specific for short-lived mice were detected. Furthermore, for males (Rikenella and Alloprevotella) and females (Lactobacillus and Bacteroides), specific bacterial groups emerged as predictors (AUC = 1), highlighting sex-specific patterns. Long-lived mice showed a strong correlation of Bacteroides (0.918) with lipid and steroid hormone metabolism, while a negative correlation of GABAergic synapse with body weight (−0.589). We found that several Bacteroides species harboring the sulfotransferase gene and gene cluster for sulfonate donor synthesis are involved in converting cholesterol to cholesterol sulfate, significantly higher in the feces of long-lived individuals. Overall, we suggest that increased involvement of gut bacteria, mainly Bacteroides spp. in cholesterol sulfate synthesis could ameliorate aging through lipid metabolism. [ABSTRACT FROM AUTHOR]

Purpose: Impaired gut barrier function is associated with systemic inflammation and many chronic diseases. Undigested dietary proteins are fermented in the colon by the gut microbiota which produces nitrogenous metabolites shown to reduce barrier function in vitro. With growing evidence of sex-based differences in gut microbiotas, we determined whether there were sex by dietary protein interactions which could differentially impact barrier function via microbiota modification. Methods: Fermentation systems were inoculated with faeces from healthy males (n = 5) and females (n = 5) and supplemented with 0.9 g of non-hydrolysed proteins sourced from whey, fish, milk, soya, egg, pea, or mycoprotein. Microbial populations were quantified using fluorescence in situ hybridisation with flow cytometry. Metabolite concentrations were analysed using gas chromatography, solid phase microextraction coupled with gas chromatography-mass spectrometry and ELISA. Results: Increased protein availability resulted in increased proteolytic Bacteroides spp (p < 0.01) and Clostridium coccoides (p < 0.01), along with increased phenol (p < 0.01), p-cresol (p < 0.01), indole (p = 0.018) and ammonia (p < 0.01), varying by protein type. Counts of Clostridium cluster IX (p = 0.03) and concentration of p-cresol (p = 0.025) increased in males, while females produced more ammonia (p = 0.02), irrespective of protein type. Further, we observed significant sex-protein interactions affecting bacterial populations and metabolites (p < 0.005). Conclusions: Our findings suggest that protein fermentation by the gut microbiota in vitro is influenced by both protein source and the donor's sex. Should these results be confirmed through human studies, they could have major implications for developing dietary recommendations tailored by sex to prevent chronic illnesses. [ABSTRACT FROM AUTHOR]

The bakery industry generates substantial food waste, leading to global environment pollution and economic losses. However, these by-products contain valuable bioactive compounds, such as melanoidins, which are brown pigmented compounds with significant antioxidant, antimicrobial and anti-inflammatory properties, making them ideal functional ingredient. This study aimed to evaluate the optimal enzymatic extraction of melanoidins from bread crust using different proteolytic enzymes: pronase E, serine-endo-protease (SP), metalloenzyme protease (MP) and endoprotease papain enzyme (EP). While the yield of melanoidins from MP and EP was lower than that of pronase E, SP yield was significantly higher. No cytotoxicity of bioaccessible, gastrointestinal and colonic fractions was observed in the cell lines Caco-2, HUVEC and SHSY5Y. The antioxidant properties and ability to stabilize the hydroxyl radical were characterized in bioaccessible fractions of the four melanoidins extracts. Moreover, melanoidins positively influenced the intestinal microbiota by increasing beneficial bacteria like Bifidobacterium and Lactobacillus, while reducing non-beneficial bacteria such as Bacteroides spp. and Clostridium leptum, with particularly significant results for SP and EP enzyme extracts. In conclusion, SP and EP enzymes appear to be viable alternatives to pronase E for obtaining melanoidin extracts as functional ingredients. These enzymes offer potential cost advantages and contribute to the sustainable utilization of bakery by-product melanoidins in various food applications. Implementing these alternatives could help to reduce food waste, environmental pollution and economic losses in the bakery industry while promoting the use of valuable bioactive compounds. [ABSTRACT FROM AUTHOR]

Breast cancer (BC) is one of the most prevalent cancers worldwide. Fortunately, BC treatment has taken a huge turn in the last few years. Despite these advances, one of the main issues related to systemic treatment remains the management of its side effects, including cardiotoxicity. In this regard, we highlight the irreversible dose-dependent cardiotoxicity of anthracyclines related to oxidative stress and the reversible cardiotoxicity with trastuzumab, whose mechanism is still poorly understood. Moreover, the combination of anthracyclines and trastuzumab further exacerbate the myocardial damage. More recently, altered gut microbiota composition has been linked to the long-term effects of cancer therapy, including the potential connection between treatment-related microbial changes and cardiotoxicity. Bacteroides spp., Coriobacteriaceae_UGC-002, and Dubosiella have already been reported as bacterial species with deleterious effects on the myocardium, mainly due to the promotion of inflammation. On the other hand, Alloprevotella, Rickenellaceae_RC9, Raoultella planticola, Klebsiella pneumoniae, and Escherichia coli BW25113 can induce cardioprotection, predominantly by increasing anti-inflammatory cytokines, promoting intestinal barrier integrity and early metabolization of doxorubicin. Herein, we explore the role of gut microbiota in the development of cardiotoxicity, as well as future perspectives to decrease the risk of cardiotoxicity associated with BC treatment. [ABSTRACT FROM AUTHOR]

Background: Human intestine microbiota are known to be directly and indirectly altered during some diseases such as kidney complications. Bacteroides is considered as the main and the most abundant phylum among human gut microbiota, which has been classified as enterotype 1. This study aimed to assess the abundance of Bacteroides spp. in fecal flora of end-stage renal disease (ESRD) and chronic kidney disease (CKD) patients and compare it with the Bacteroides composition among fecal flora of healthy individual. Methods: Fresh fecal samples were collected from 20 CKD/ESRD patients and 20 healthy individual without any kidney complications. The pure microbial DNA was extracted by QIAamp Stool Mini Kit from stool samples. MiSeq system was used to analyze the intestinal composition by next generation sequencing method. Results: A number of 651 bacterial strains were isolated and identified from 40 fecal samples of both patients and healthy groups. Bioinformatics analysis defined 18 different types of Bacteroides species which included 2.76% of all strains. Statistical analysis showed no significant difference between study groups (P > 0.05). In both healthy and patient groups three species including B. dorei, B. uniformis, and B. ovatus have allocated the most abundance to themselves. The lowest abundance was related to B. eggerthii, A. furcosa and B. barnesiae among CKD/ESRD patients and A. furcosa, B. barnesiae, and B. coprocola had the lowest abundance among healthy people. Conclusion: This study indicates despite all previous evidence of Bacteroides role in gut microbiota, it had no different distribution between healthy persons and CKD/ESRD patients. [ABSTRACT FROM AUTHOR]

Many factors underlie the development of inflammatory bowel disease (IBD) in humans. In particular, imbalance of microbiota and thinning of the mucosal layer in the large intestine play a huge role. Pathogenic microorganisms also exacerbate the course of diseases. In this research the role of mucin 2 deficiency in the formation of intestinal microflora in the experimental model using the Muc2 gene knockout mice in the presence of Helicobacter spp. was investigated. Also, restorative and anti-inflammatory effect of the dietary L-fucose in the Muc2–/– mice on microflora and immunity was evaluated. For this purpose, bacterial diversity in feces was studied in the animals before and after antibiotic therapy and role of the dietary L-fucose in their recovery was assessed. To determine the effect of bacterial imbalance and fucose on the immune system, mRNA levels of the genes encoding pro-inflammatory cytokines (Tnf, Il1a, Il1b, Il6) and transcription factors of T cells (Foxp3 – Treg, Rorc – Th17, Tbx21 – Th1) were determined in the colon tissue of the Muc2–/– mice. Significant elimination of bacteria due to antibiotic therapy caused decrease of the fucose levels in the intestine and facilitated reduction of the regulatory T cell transcription factor (Foxp3). When the dietary L-fucose was added to antibiotics, the level of bacterial DNA of Bacteroides spp. in the feces of the Muc2–/– mice was partially restored. T regulatory cells are involved in the regulation of inflammation in the Muc2–/– mice. Antibiotics reduced the number of regulatory T cell but did not decrease the inflammatory response to infection. Fucose, as a component of mucin 2, helped to maintain the level of Bacteroides spp. during antibiotic therapy of the Muc2–/– mice and restored biochemical parameters, but did not affect the inflammatory response. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the fermentation characteristics of proteins from diverse sources by human gut microbiota. Cereal proteins (rice and oat), red meat proteins (pork and beef), chicken protein and casein were selected as the substrates for simulated gastrointestinal digestion (SGID), and human faecal samples were collected from healthy donors as the inoculum of fermentation. In this study, we further analyzed the correlations of amino acids (AA) compositions, fermentation productions and gut microbiota. As the results, the animal protein groups had higher degree of hydrolysis (DH) after digestion and higher levels of ammonia nitrogen (NH3-N) after fermentation than cereal proteins. The pH value of fermentation liquid declined as proteins were added during fermentation. Cereal protein groups promoted the gut microbiota to produce more short chain fatty acids (SCFAs) with the high proportion of acetate, propionate and butyrate by lowering the pH than red meat proteins. The abundance of Firmicutes at phylum level in cereal protein groups was lower than red meat proteins after fermentation. The cereal protein groups enhanced the growth of Bacteroides spp. and Bifidobacterium spp. while red meat proteins stimulated the growth of Peptoclostridium spp.. Taken together, our research implies that cereal proteins have better fermentation characters than red meat proteins. [ABSTRACT FROM AUTHOR]

Background: The gut microbiota plays an important role in human health, as it can affect host immunity and susceptibility to infectious diseases. Invasive intestinal candidiasis is strongly associated with gut microbiota homeostasis. However, the nature of the interaction between Candida albicans and gut bacteria remains unclear. Objective: This review aimed to determine the nature of interaction and the effects of gut bacteria on C. albicans so as to comprehend an approach to reducing intestinal invasive infection by C. albicans. Methods: This review examined 11 common gut bacteria's interactions with C. albicans, including Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Enterococcus faecalis, Staphylococcus aureus, Salmonella spp., Helicobacter pylori, Lactobacillus spp., Bacteroides spp., Clostridium difficile, and Streptococcus spp. Results: Most of the studied bacteria demonstrated both synergistic and antagonistic effects with C. albicans, and just a few bacteria such as P. aeruginosa, Salmonella spp., and Lactobacillus spp. demonstrated only antagonism against C. albicans. Conclusions: Based on the nature of interactions reported so far by the literature between gut bacteria and C. albicans, it is expected to provide new ideas for the prevention and treatment of invasive intestinal candidiasis. [ABSTRACT FROM AUTHOR]

Non-alcoholic steatohepatitis (NASH) is a more dangerous form of chronic non-alcoholic fatty liver disease (NAFLD). In the current investigation, the influence of citicoline on high-fat diet (HFD)-induced NASH was examined, both alone and in combination with Lactobacillus (probiotic). NASH was induced by feeding HFD (10% sugar, 10% lard stearin, 2% cholesterol, and 0.5% cholic acid) to rats for 13 weeks and received single i.p. injection of streptozotocin (STZ, 30 mg/kg) after 4 weeks. Citicoline was given at two dose levels (250 mg and 500 mg, i.p.) at the beginning of the sixth week, and in combination with an oral suspension of Lactobacillus every day for eight weeks until the study's conclusion. HFD/STZ induced steatohepatitis as shown by histopathological changes, elevated serum liver enzymes, serum hyperlipidemia and hepatic fat accumulation. Moreover, HFD convinced oxidative stress by increased lipid peroxidation marker (MDA) and decreased antioxidant enzymes (GSH and TAC). Upregulation of TLR4/NF-kB and the downstream inflammatory cascade (TNF-α, and IL-6) as well as Pentaraxin, fetuin-B and apoptotic markers (caspase-3 and Bax) were observed. NASH rats also had massive increase in Bacteroides spp., Fusobacterium spp., E. coli, Clostridium spp., Providencia spp., Prevotella interrmedia, and P. gingivalis while remarkable drop in Bifidobacteria spp. and Lactobacillus spp. Co-treatment with citicoline alone and with Lactobacillus improve histopathological NASH outcomes and reversed all of these molecular pathological alterations linked to NASH via upregulating the expression of Nrf2/HO-1 and downregulating TLR4/NF-kB signaling pathways. These results suggest that citicoline and lactobacillus may represent new hepatoprotective strategies against NASH progression. [ABSTRACT FROM AUTHOR]

Background: Clostridioides difficile infection (CDI) has a high recurrent infection rate. Faecal microbiota transplantation (FMT) has been used successfully to treat recurrent CDI, but much remains unknown about the human gut microbiota response to replacement therapies. In this study, antibiotic-mediated dysbiosis of gut microbiota and bacterial growth dynamics were investigated by two quantitative methods: real-time quantitative PCR (qPCR) and direct culture enumeration, in triple-stage chemostat models of the human colon. Three in vitro models were exposed to clindamycin to induce simulated CDI. All models were treated with vancomycin, and two received an FMT. Populations of total bacteria, Bacteroides spp., Lactobacillus spp., Enterococcus spp., Bifidobacterium spp., C. difficile, and Enterobacteriaceae were monitored using both methods. Total clostridia were monitored by selective culture. Using qPCR analysis, we additionally monitored populations of Prevotella spp., Clostridium coccoides group, and Clostridium leptum group. Results: Both methods showed an exacerbation of disruption of the colonic microbiota following vancomycin (and earlier clindamycin) exposure, and a quicker recovery (within 4 days) of the bacterial populations in the models that received the FMT. C. difficile proliferation, consistent with CDI, was also observed by both qPCR and culture. Pearson correlation coefficient showed an association between results varying from 98% for Bacteroides spp., to 62% for Enterobacteriaceae. Conclusions: Generally, a good correlation was observed between qPCR and bacterial culture. Overall, the molecular assays offer results in real-time, important for treatment efficacy, and allow the monitoring of additional microbiota groups. However, individual quantification of some genera (e.g. clostridia) might not be possible without selective culture. [ABSTRACT FROM AUTHOR]

Objective: Probiotics and nutrient intakes modulate gastrointestinal (GIT) microbiota and symptoms of irritable bowel syndrome (IBS). The extent to which these factors influence the microbiota is relatively unknown. The primary objective of this paper was to investigate the effect of a probiotic on gut microbiota and IBS symptoms. The secondary objective was exploring correlations between dietary intake and gut microbiota. Design: This study was an extension of a randomised clinical trial (Clinical Trials Registry NCT018867810). Dietary intake was recorded by three-day estimated food records. Faecal samples were collected at three time points: (1) baseline (A), (2) after eight weeks' probiotic supplementation (Lactobacillus plantarum 299v) (B) and (3) following a two-week washout period (C). Total Bacteroides spp., Bifidobacteria bifidum and Lactobacillus plantarum were quantified by quantitative real-time polymerase chain reaction (qPCR). Results: Twenty-eight diarrhoea-predominant IBS (D-IBS) and 24 constipation-predominant IBS (C-IBS) patients participated. Lactobacillus plantarum profiles at baseline (A) were significantly different between C-IBS and D-IBS (−0.956 ± 1.239 vs. −1.700 ± 1.239; p = 0.024). There was no significant change in bacterial counts after completion of the trial (B) and following the washout period (C) between groups. In both groups there were significant direct correlations between fibre and Lactobacillus plantarum and inverse correlations between fibre and Bacteroides spp. There was no difference in symptom severity scores between treatment and placebo groups during the study. Conclusion: The probiotic had no effect on symptoms and GIT microbiota. Certain nutrients strongly correlate to certain bacterial profiles, suggesting that nutrients can significantly influence gastrointestinal microbiota composition. [ABSTRACT FROM AUTHOR]

Inbred mouse strains KK.Cg-a/a and KK.Cg-Ay/a known as genetic models of type 2 diabetes mellitus significantly surpassed the control strain C57BL/6J in the body weight, relative weight of extractable fat, and basal blood glucose levels. Real-timePCR of fecal samples from KK.Cg-a/a and KK.Cg-Ay/a mice revealed dysbiosis typical of type 2 diabetes mellitus in humans and animals. Long-term intragastric administration of a suspension of Hafnia alvei bacteria had no effect on the above morphometric and biochemical parameters. At the same time, recovery of the Bacteroides spp. population in KK.Cg-Ay/a mice and a decrease in the number of Bifidobacterium spp. in KK.Cg-a/a mice were observed. The possibility of therapeutic use of the probiotic based on H. alvei is discussed. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis‐associated interstitial lung disease (RA‐ILD) is a serious and common extra‐articular disease manifestation. Patients with RA‐ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole‐metagenome shotgun sequencing on fecal samples from 30 patients with RA‐ILD, and 30 with RA‐non‐ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference‐based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA‐ILD and RA‐non‐ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA‐ILD), Gemmiger formicilis, and Ruminococcus bromii (RA‐non‐ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA‐ILD and RA‐non‐ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA‐ILD and RA‐non‐ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research. [ABSTRACT FROM AUTHOR]

Background: The global pandemic of coronavirus disease 2019 (COVID-19) continues to affect people around the world, with one of the most frequent comorbidities being Type 2 Diabetes (T2D). Studies have suggested a link between disbalances in gut microbiota and these diseases, as well as with COVID-19, potentially due to inflammatory dysfunction. This study aims to analyze the changes in gut microbiota in COVID-19 patients with T2D using a culture-based method. Methods: The stool samples were taken from 128 patients with confirmed COVID19. Changes in the composition of gut microbiota were analyzed by culture-based method. The study used chi-squared and t-test to find significant differences in gut bacteria between samples and non-parametric correlation analysis to examine relationship between gut bacteria abundance, C‐reactive protein (CRP) levels and length of stay (LoS) in COVID-19 patients without T2D. Results: The gut microbiota of T2D patients with COVID-19 showed increased Clostridium spp., Candida spp., and decreased Bifidobacterium spp., Lactobacillus spp. Metformin-treated patients with T2D and COVID-19 without antibiotic treatment showed increased Bacteroides spp., Lactobacillus spp., and decreased Enterococcus, Clostridium compared to the same group with antibiotic treatment. The study also found a positive correlation between the abundance of certain gut microbiota genera, such as Klebsiella spp. and Enterococcus spp., and CRP levels and LoS in COVID-19 patients without and with T2D, while the abundance of other genera, such as Bifidobacterium spp. and Lactobacillus spp., was found to have a negative correlation. Conclusion: In conclusion, this study provides important insights into the gut microbiota composition of SARS-CoV-2-infected individuals with T2D and its potential impact on the course of the disease. The findings suggest that certain gut microbiota genera may be associated with increased CRP levels and longer hospital stays. The significance of this study lies in the fact that it highlights the potential role of gut microbiota in the progression of COVID-19 in patients with T2D, and may inform future research and treatment strategies for this patient population. The future impact of this study could include the development of targeted interventions to modulate gut microbiota in order to improve outcomes for COVID-19 patients with T2D. [ABSTRACT FROM AUTHOR]

Background: Ginsenoside compound K (GC-K) potentially alleviates ulcerative colitis involved in gut microbiota, which is significantly associated with the occurrence and development of colitis. However, the effect and mechanism of GC-K on anti-colitis in relation to gut microbiota are not clear. This study focused on the prevention and mechanism of GC-K on Dextran sulfate sodium (DSS)-induced colitis of mice pertinent to gut microbiota. Methods: DSS was used to establish a chronic colitis mouse model. Body weight analysis, colon length measurement, HE staining, and inflammatory factors levels were processed in animal experiments. Flow cytometry was employed to analyze Th17/Treg cells in the mouse spleen and blood. 16S rRNA sequencing was utilized to analyze gut microbiota. Fecal microbiota transplantation (FMT) experiment was employed to verify the anti-colitis efficacy of GC-K by reshaping gut microbiota. Results: GC-K significantly relieved colitis-related symptoms due to decreased disease activity index (DAI) scores, spleen weight, and increased colon length. Additionally, the tight junction proteins were increased, and the pro-inflammatory cytokines, such as TNF-α, IL-6, IL-1β and IL-17, were decreased after GC-K treatment. Furthermore, Bacteroides spp. significantly increased after modeling. Moreover, FMT experiments confirmed that GC-K-driven gut microbiota greatly relieved DSS-induced colitis. Conclusion: GC-K alleviated colitis via the modulation of gut microbiota. Highlights: Ginsenoside Compound K (GC-K) alleviated colitis in DSS-induced Mice. GC-K modulated gut microbiota in DSS-induced mice. GC-K relieved colitis via regulating gut microbiota. GC-K-driven gut microbial effectively ameliorated colitis. [ABSTRACT FROM AUTHOR]

The appropriate domestic cooking methods can retain and protect the biological properties of foods well. Thus, the objective of this study was to unravel the effect of different cooking methods on the microbiota modulatory properties of yam and their non-starch polysaccharides by an in vitro simulated digestion and fermentation model. The results showed that different cooking processes led to different changes in polysaccharide content. The polysaccharide content of yam increased by 21.3~108.2% or decreased by 12.0% compared with that of raw yam. Additionally, the soluble polysaccharides contents in all cooked yam samples significantly increased by 16.85~119.97% after in vitro digestion. The regulation of whole-yam digesta on gut microbiota was partly related with yam polysaccharides. Both yam and yam polysaccharide fermentation appeared to promote beneficial bacteria, such as Bifidobacteria, Bacteroides spp. and Megasphaera and suppressed bacterial pathogens such as Ruminococcusforques and Escherichia-Shigella. Household cooking significantly influenced the prebiotic performances of yam and yam polysaccharides by changing the heat-sensitive microbial substrates and their physiology properties. According to our results, normal-pressure steaming and normal-pressure boiling processes can retain the microbiota modulatory effects of Chinese yam. [ABSTRACT FROM AUTHOR]

Background and aim: Gut microbiota (GM) can support colorectal cancer (CRC) progression by modulating immune responses through the production of both immunostimulatory and/or immunosuppressive cytokines. The role of IL-9 is paradigmatic because it can either promote tumor progression in hematological malignancies or inhibit tumorigenesis in solid cancers. Therefore, we investigate the microbiota–immunity axis in healthy and tumor mucosa, focusing on the correlation between cytokine profile and GM signature. Methods: In this observational study, we collected tumor (CRC) and healthy (CRC-S) mucosa samples from 45 CRC patients, who were undergoing surgery in 2018 at the Careggi University Hospital (Florence, Italy). First, we characterized the tissue infiltrating lymphocyte subset profile and the GM composition. Subsequently, we evaluated the CRC and CRC-S molecular inflammatory response and correlated this profile with GM composition, using Dirichlet multinomial regression. Results: CRC samples displayed higher percentages of Th17, Th2, and Tregs. Moreover, CRC tissues showed significantly higher levels of MIP-1α, IL-1α, IL-1β, IL-2, IP-10, IL-6, IL-8, IL-17A, IFN-γ, TNF-α, MCP-1, P-selectin, and IL-9. Compared to CRC-S, CRC samples also showed significantly higher levels of the following genera: Fusobacteria , Proteobacteria , Fusobacterium , Ruminococcus2 , and Ruminococcus. Finally, the abundance of Prevotella spp. in CRC samples negatively correlated with IL-17A and positively with IL-9. On the contrary, Bacteroides spp. presence negatively correlated with IL-9. Conclusions: Our data consolidate antitumor immunity impairment and the presence of a distinct microbiota profile in the tumor microenvironment compared with the healthy mucosa counterpart. Relating the CRC cytokine profile with GM composition, we confirm the presence of bidirectional crosstalk between the immune response and the host's commensal microorganisms. Indeed, we document, for the first time, that Prevotella spp. and Bacteroides spp. are, respectively, positively and negatively correlated with IL-9, whose role in CRC development is still under debate. [ABSTRACT FROM AUTHOR]

Objectives: The approval of new antibiotics is essential to combat infections caused by antimicrobial-resistant pathogens; however, such agents should be tested to determine their effect on the resident microbiota and propensity to select for opportunistic pathogens, such as Clostridioides difficile. Eravacycline is a new antibiotic for the treatment of complicated intra-abdominal infections. Here, we determined the effects of eravacycline compared with moxifloxacin on the microbiota and if these were conducive to induction of C. difficile infection (CDI).Methods: We seeded in vitro chemostat models, which simulate the physiological conditions of the human colon, with a human faecal slurry and instilled gut-reflective concentrations of either eravacycline or moxifloxacin.Results: Eravacycline instillation was associated with decreased Bifidobacterium, Lactobacillus and Clostridium species, which recovered 1 week after exposure. However, Bacteroides spp. levels decreased to below the limit of detection and did not recover prior to the end of the experiment. Post-eravacycline, a bloom of aerobic bacterial species occurred, including Enterobacteriaceae, compared with pre-antibiotic, which remained high for the duration of the experiment. These changes in microbiota were not associated with induction of CDI, as we observed a lack of C. difficile spore germination and thus no toxin was detected. Moxifloxacin exposure sufficiently disrupted the microbiota to induce simulated CDI, where C. difficile spore germination, outgrowth and toxin production were seen.Conclusions: These model data suggest that, despite the initial impact of eravacycline on the intestinal microbiota, similar to clinical trial data, this novel tetracycline has a low propensity to induce CDI. [ABSTRACT FROM AUTHOR]

Bacteroides spp. are part of the human intestinal microbiota but can under some circumstances become clinical pathogens. Phages are a potentially valuable therapeutic treatment option for many pathogens, but phage therapy for pathogenic Bacteroides spp. including Bacteroides fragilis is currently limited to three genome-sequenced phages. Here we describe the isolation from sewage wastewater and genome of a lytic phage, vB_BfrS_23, that infects and kills B. fragilis strain GB124. Transmission electron microscopy identified this phage as a member of the Siphoviridae family. The phage is stable when held at temperatures of 4 and 60°C for 1 h. It has a very narrow host range, only infecting one host from a panel of B. fragilis strains (n = 8). Whole-genome sequence analyses of vB_BfrS_23 determined it is double-stranded DNA phage and is circularly permuted, with a genome of 48,011 bp. The genome encodes 73 putative open reading frames. We also sequenced the host bacterium, B. fragilis GB124 (5.1 Mb), which has two plasmids of 43,923 and 4,138 bp. Although this phage is host specific, its isolation together with the detailed characterization of the host B. fragilis GB124 featured in this study represent a useful starting point from which to facilitate the future development of highly specific therapeutic agents. Furthermore, the phage could be a novel tool in determining water (and water reuse) treatment efficacy, and for identifying human fecal transmission pathways within contaminated environmental waters and foodstuffs. [ABSTRACT FROM AUTHOR]

This article explores the effects of different oral antidiabetic drugs (OADs) on the gut microbiota in patients with type 2 diabetes (T2D). The study found that acarbose and berberine had significant impacts on the gut microbiota, while metformin, vildagliptin, and glipizide did not. The baseline gut microbiota was found to be associated with the response to OAD treatment. However, the study acknowledges that there are variations in the reported gut microbial alterations due to factors such as ethnicity, sample size, and methodology. Further research is needed to fully understand the interactions between OADs and the gut microbiota and their potential impact on drug efficacy. [Extracted from the article]

In recent years, many studies have shown that the gut microbiota can affect the occurrence and development of a variety of human diseases. A variety of skin diseases are related to the regulation of the gut-skin axis, such as psoriasis, atopic dermatitis, and acne. Gut microbial dysbiosis can promote the development of these diseases. The gut microbiota can affect estrogen metabolism, ß-glucuronidase secreted by the gut microbiota can promote the reabsorption of estrogen by the gut, and estrogen is transported to other parts of the body through the circulatory system. The occurrence and development of melasma are closely related to abnormal metabolism of estrogen. The relationship between the structure of the gut microbiota and melasma remains unclear. Epidemiological surveys were conducted in patients with melasma and healthy subjects (control group) in this study. The feces were collected for 16S rRNA sequencing analysis of the gut microbiota. To compare the similarities and differences in species diversity of the gut microbiota between these two groups, we calculated the a-diversity and ß-diversity indices and analyzed the differences between them. We found that the abundance of Collinsella spp., Actinomyces spp. (belonging to Actinobacteria), Parabacteroides spp., Bacteroides spp., Paraprevotella spp. (belonging to Bacteroidetes), Blautia spp., and Roseburia spp. (belonging to Firmicutes) in the melasma group were significantly different compared with that in the healthy group. The largest difference was found in Actinobacteria (p < 0.05), and there were also significant differences in the abundance of Coriobacteriia, Actinobacteria, Coriobacteriales, Coriobacteriaceae, and Collinsella spp. between the two groups (all p < 0.05). Many of these differences in the microbiota were closely related to the production of ß-glucuronidase and the regulation of estrogen synthesis or metabolism. Changes in the gut microbiota structure and the biological effects of Collinsella spp. in the microbiota in patients with melasma can play an important role in the occurrence and development of melasma by affecting the body's estrogen metabolism. This study provides a theoretical basis and experimental data reference for future studies on the relationship between the gut microbiota and melasma, and may be helpful for the prevention and treatment of melasma. [ABSTRACT FROM AUTHOR]

The intestinal epithelium surface is covered by a layer of mucus that harbors a complex and dynamic population of bacteria termed gut microbiota. In particular, some gut bacteria have the ability to degrade the mucin glycan for nutritional sources. However, the bacterial diversity of mucin-degrading bacteria in human gut microbiota and their role in the gut remains unclear. In this study, we characterized the diversity of mucin-degrading bacteria in the human gut microbiota by an established cultivation-based molecular profiling method. The results showed the gut commensals having the mucin degrading ability were widely distributed in the gut microbiota and were more abundant than previously thought. In addition, many previously uncharacterized mucin degraders were isolated from faecals samples, suggesting the mucindegrading gut commensals were underappreciated. To gain a better understanding of the interaction between these mucin-degrading gut commensals and the host, the effect of the commensals on intestinal epithelial cells were examined, and the results revealed that the commensals (8 Bacteroides spp., 2 Parabacteroides spp, Akkermanisa muciniphila and Bifidobacterial dentium) incited low level of inflammatory response (IL-8 and TNF-a) but suppressed the inflammatory response induced by E. coli through downregulating the NF-kB pathway. The presence of gut commensals also showed potential in enhancing the epithelial tight junction (TJ) barrier function through regulating the mRNA expression of TJ protein genes such as Zo-1, Occludin, Claudin-1 and E-cadherin. Furthermore, the presence of commensal bacteria P. distasonis, B. thetaiotaomicron and A. muciniphila completely or partly restored the pro-inflammatory cytokine IL-1b induced TJ barrier disruption. In conclusion, these findings indicate that mucin-degrading gut commensals were widely distributed in the gut microbiota and showed antiinflammatory effect against pathogen infection and potential in modulating the epithelial barrier function. [ABSTRACT FROM AUTHOR]

1. The purpose of this study was to see how dietary supplementation with phenylpyruvate affected broiler growth, slaughter performance, gut health microbiota and immunity. This information can be used to develop alternative approaches to antibiotic replacement in modern poultry production and health. 2. A total of 288, one-day-old broiler chickens were randomly assigned to one of four groups (six replicates each replicate has 12 chickens). A control basal diet (NC), basal diet plus antibiotic virginiamycin 15ppm (PC), basal diet plus phenylpyruvate 1 kg/t or 2 kg/t, respectively (LCP and HCP). 3. Results showed that the birds in the PC group had higher ADFI during the first 21 d, and better FCR than the NC group. The HCP-fed group had a higher all-eviscerated ratio than the NC group and less abdominal fat than the birds fed LCP. The birds fed HCP had increased villus length and crypt depth in the ileum compared to the NC group. 4. The bursa index was lower in the HCP group whereas the thymus index was lower in LCP and PC groups. In contrast, birds fed HCP has lower pro-inflammatory cytokine IL-1, as well as lower TLR4. Phenylpyruvate improved number in the Selenomonadaceae, genus Megamonas bacteroides spp., which are known for their beneficial effects on the maintenance of the cell surface structure, regulating aromatic amino acids and Clostridia jejuni-suppressive treatment respectively. 5. It was concluded that phenylpyruvate can be utilised in feed to improve growth performance and positively modulate gut microbiota. However, this was less efficient than antibiotics in improving growth performance, although more efficient in improving productive performance and gut morphology. Moreover, a high dose of phenylpyruvate is more effective than a low dose. [ABSTRACT FROM AUTHOR]

Whole cereal grains are excellent sources of both soluble and insoluble fibers, which collectively promote a healthy gut microbiota and reduce the risk of chronic diseases. However, the metabolic interactions between soluble and insoluble fibers derived from whole grains remain poorly understood. This study investigated the in vitro fermentability of soluble β-glucans (BG), predigested barley bran (PBB), and a combination of PBB and BG (PBB_BG) using ten human fecal samples. The pH values of BG and PBB_BG in all ten donors sharply decreased within 12 h post-fermentation, accompanied by a marked increase in acetate in the BG and PBB_BG groups, but not in the PBB group. This suggests that BG were rapidly degraded by various gut microbiota, and the slow-fermenting PBB had a negligible impact on BG degradation. At 48 h post-fermentation, PBB_BG significantly enhanced propionate and butyrate production compared with BG or PBB, with the highest levels of propionate and butyrate observed in eight out of ten donors and all ten donors, respectively. Notably, the addition of BG consistently and substantially increased propionate and butyrate production in donors 1, 2 and 10. Analysis of microbiota in liquid medium and insoluble bran-attached microbiota revealed that BG stimulated different Bacteroides spp. in the liquid phase across all ten donors, while uniquely inhibiting bran-attached Prevotella spp. in donors 1, 2 and 10. Additionally, BG induced donor-dependent enrichments of bran-attached propionate- and butyrate-producing microbes. These results suggest that fast-fermenting β-glucans can donor-dependently enhance the fermentability of slow-fermenting bran fibers, highlighting the importance of personalized microbiota responses in whole grain interventions. [Display omitted] • Various microbiota degrade soluble β-glucans more rapidly than insoluble brans. • Degradation of soluble β-glucans is unaffected by the presence of insoluble brans. • Fast-fermenting β-glucans enhance the fermentability of slow-fermenting brans in a donor-dependent manner. • Soluble β-glucans effectively and donor-dependently enrich Bacteroides spp. and Prevotella spp. in liquid medium. • Replacement of bran-attached Prevotella spp. with SCFA-producing microbes increases bran fermentability. [ABSTRACT FROM AUTHOR]

The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients. [ABSTRACT FROM AUTHOR]

The microbiome is an important player within physiological homeostasis of the body but also in pathophysiological derailments. Chronic social stress is a challenge to the organism, which results in psychological illnesses such as depression in some individuals and can be counterbalanced by others, namely resilient individuals. In this study, we wanted to elucidate the potential contribution of the microbiome to promote resilience. Male mice were subjected to the classical chronic social defeat paradigm. Defeated or undefeated mice were either controls (receiving normal drinking water) or pre-treated with antibiotics or probiotics. Following social defeat, resilient behavior was assessed by means of the social interaction test. Neither depletion nor probiotic-shifted alteration of the microbiome influenced stress-associated behavioral outcomes. Nevertheless, clear changes in microbiota composition due to the defeat stress were observed such as elevated Bacteroides spp. This stress-induced increase in Bacteroides in male mice could be confirmed in a related social stress paradigm (instable social hierarchy) in females. This indicates that while manipulation of the microbiome via the antibiotics- and probiotics-treatment regime used here has no direct impact on modulating individual stress susceptibility in rodents, it clearly affects the microbiome in the second line and in a sex-independent manner regarding Bacteroides. [ABSTRACT FROM AUTHOR]

Objective: To determine whether there is an association between the inflammatory potential of the diet, measured by the dietary inflammatory index (DII®), and the composition of intestinal microbiota in adults with functional constipation (FC). Methods: A cross-sectional study was carried out with 68 adults with FC. Energy-adjusted DII (E-DII) was calculated from data obtained from food surveys, serum inflammation markers were measured and the composition of the intestinal microbiota was evaluated using the 16S rRNA gene sequencing method. Participants were assigned into two groups: anti-inflammatory diet (AD: E-DII < 0) and pro-inflammatory diet (PD: E-DII ≥ 0). Associations of E-DII scores with microbial diversity and composition were examined using differences between the E-DII groups and linear and hierarchical regression. Results: E- DII was inversely correlated with relative abundance of Hungatella spp. and Bacteroides fragilis and positively correlated with Bacteroides thetaiotaomicron and Bacteroides caccae (p < 0.05). B. fragilis was positively correlated with IL-10. The AD group had higher relative abundances for the genus Blautia and Hungatella, lower abundances of Bacteroides thetaiotamicron and Bacteroides spp. (p < 0.05), as well as higher frequency of evacuation (p = 0.02) and lower use of laxatives (p = 0.05). The AD group showed a reduction in the abundance of Desulfovibrio spp. and Butyrivibrio, Butyrivibrio crossotus, Bacteroides clarus, Bacteroides coprophilus and Bacteroides intestinalis (all p < 0.05). The greater abundance of Bacteroides clarus increased the individual's chance of performing a manual evacuation maneuver. Conclusion: Therefore, the results of this study demonstrated that the inflammatory potential of the diet is associated with the gut microbiota in individuals with FC. [ABSTRACT FROM AUTHOR]