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Yin-Chen-Hao Tang (YCHT), consisting of Artemisia annua L., Gardenia jasminoides Ellis, and Rheum Palmatum L., has been used to relieve liver diseases in China for thousands of years. Several protective mechanisms of YCHT on liver injury have been investigated based on metabolomics, but the effects of YCHT on the alterations in the gut microbiota are still unclear. In this study, an integrated approach based on 16S rRNA gene sequencing combined with high-performance liquid chromatography-mass spectrometry (HPLC-MS) metabolic profiling was performed to assess the effects of YCHT on liver injury induced by carbon tetrachloride (CCl4) through the regulation of the relative abundances of gut microbiota and their relationships with biomarker candidates. A total of twelve significantly altered bacterial genera and nine metabolites were identified, which returned to normal levels after YCHT treatment. The relative abundances of the identified microbiota, including significantly elevated amounts of p_Firmicutes, c_Clostridia, o_Clostridiales, f_Ruminococcaceae, g_[Eubacterium]_coprostanoligenes_group, s_uncultured_bacterium_f_Lachnospiraceae and remarkedly increased amounts of p_Bacteroidetes, c_Bacteroidia, o_Bacteroidales, f_Bacteroidaceae, g_Bacteroides and s_uncultured_bacterium_g_Bacteroides, were found in model rats compared with controls. Potential biomarkers, including lower levels of LysoPC (16:1(9Z)/0:0), LysoPC (20:3(5Z,8Z,11Z)), LysoPC (17:0), LysoPC (20:1(11Z)) and 3-hydroxybutyric acid and higher amounts of ornithine, L-kynurenine, hippuric acid and taurocholic acid are involved in several custom metabolic pathways, such as arginine and proline metabolism, tryptophan metabolism, glycerophospholipid metabolism and primary bile acid biosynthesis. Interestingly, there was a strong correlation between the perturbed gut microbiota in genera c_Clostridia and o_Clostridiales and the altered plasma metabolite 3-hydroxybutyric acid. This finding means that the hepatoprotective effects of YCHT may be due to the regulation of the production of the functional metabolite 3-hydroxybutyric acid through changes in the proportions of c_Clostridia and o_Clostridiales. These results showed that the hepatoprotective effects of YCHT not only focused on custom metabolic pathways but also depended on the changes in the gut microbiota in liver injury. These findings suggest that the 16S rRNA gene sequencing and LC-MS based metabolomics approach can be applied to comprehensively evaluate the effects of traditional Chinese medicines (TCMs).

Infectious process even at the initial stage after aerosol infection with Mycobacterium tuberculosis induced rapid changes in vaginal microbiota in mice. Rapid decrease in both the quantity and diversity of microbiota was noted, and then, partial recovery of normal flora was observed. Changes in vaginal microbiota was detected as soon as in 3-7 days after lung infection, while inflammatory changes appeared by day 35. At the early stage of infection, no signs of inflammation were observed, neither M. tuberculosis nor its DNA were detected in mouse genital organs.

Background Inflammation is a hallmark of prostate cancer (PCa), yet no pathogenic agent has been identified. Men from Africa are at increased risk for both aggressive prostate disease and infection. We hypothesize that pathogenic microbes may be contributing, at least in part, to high‐risk PCa presentation within Africa and in turn the observed ethnic disparity. Methods Here we reveal through metagenomic analysis of host‐derived whole‐genome sequencing data, the microbial content within prostate tumor tissue from 22 men. What is unique about this study is that patients were separated by ethnicity, African vs European, and environments, Africa vs Australia. Results We identified 23 common bacterial genera between the African, Australian, and Chinese prostate tumor samples, while nonbacterial microbes were notably absent. While the most abundant genera across all samples included: Escherichia, Propionibacterium, and Pseudomonas, the core prostate tumor microbiota was enriched for Proteobacteria. We observed a significant increase in the richness of the bacterial communities within the African vs Australian samples (t = 4.6‐5.5; P = .0004‐.001), largely driven by eight predominant genera. Considering core human gut microbiota, African prostate tissue samples appear enriched for Escherichia and Acidovorax, with an abundance of Eubacterium associated with host tumor hypermutation. Conclusions Our study provides suggestive evidence for the presence of a core, bacteria‐rich, prostate microbiome. While unable to exclude for fecal contamination, the observed increased bacterial content and richness within the African vs non‐African samples, together with elevated tumor mutational burden, suggests the possibility that bacterially‐driven oncogenic transformation within the prostate microenvironment may be contributing to aggressive disease presentation in Africa.

Background . The prevalence of urinary tract infections (UTIs) in general and recurrent lower UTIs, in particular, constantly remains at a high level. Currently, more and more researchers are attempting to study the microbial biocenosis of the urinary tract in patients with UTIs in terms of the relationship between UTIs and patient's colon microbiota in order to detail the etiology and pathogenesis of these conditions as an insufficiently studied issue. Objectives. To study the microbiota of urine and colon, as well as significant correlations in these biotopes. Materials and methods . 169 patients with recurrent lower UTIs from the Urology Clinic and the Department of Microbiology and Virology No. 1 (Rostov State Medical University) were examined. Average age: 36.2 ± 4.7 years. Midstream urine samples for bacteriological examination was taken in accordance with the rules set out in the Clinical recommendations (2014) exactly observing the preanalytical stage. The study of the colon microbiota as well as the collection of material was carried out in accordance with the rules set forth in the industry standard (OS) OST 915000. 11.0004 - 2003, Order of the Ministry of Health of the Russian Federation No. 231 of 09/09/03. Guided by this standard, the interpretation of the results was conducted. Results' statistical processing was implemented using the SPSS version 23 package. Results. In patients with recurrent lower UTIs two significant quantitative correlation coefficients were detected. The first correlation coefficient showed inverse correlation between typical E. coli isolated from urine and Eubacterium spp. isolated from feces (r = -0.434, p = 0.009). The second correlation coefficient showed a direct correlation between the amount of Lactobacilli isolated from urine and Coalulase-negative Staphylococci (CoNS) isolated from feces, accordingly (r = -0.434, p = 0.009). When comparing the frequencies of detection of various microbiota taxa, three significant correlation coefficient were found in the loci under study: between Lactobacilli or Peptococci isolated from urine and CoNS verified in feces (PCC - 0.342, p = 0.031 and PCC - 0.341, p = 0.018, respectively), as well as between Peptococci detected in urine and Enterococci in feces (PCC - 0.349, p = 0.028). Conclusion. The data we obtained on significant correlation coefficients between microorganisms isolated from urine and colon indirectly confirm the translocation mechanism. Undoubtedly, further research is needed to study the mechanism of translocation of microorganisms from the intestines and other biotopes into the organs of the urinary system in order to understand the pathogenesis of this common group of diseases.

Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity after upfront treatment have superior outcomes compared with those who remain MRD+. Recently, associations have been shown between specific commensal microbes and development of plasma cell disorders. Here, we report the association between intestinal microbiota composition and treatment outcome in MM. Microbiota composition of fecal samples collected from 34 MM patients after induction therapy and at the time of flow cytometry–based bone marrow MRD testing was determined by 16S ribosomal RNA sequencing. We observed a higher relative abundance of Eubacterium hallii in the 16 MRD− patients relative to the 18 MRD+ patients. No association was observed between microbial relative abundance and autologous stem cell transplantation history or MM paraprotein isotype. No differences in microbiota α diversity were observed between MRD− and MRD+ patients. The potential association of microbiota composition with treatment response in MM patients is an important parameter for additional correlative and clinical investigation.

The gut microbiota plays an important role in the development and progression of colorectal cancer (CRC). To learn more about the dysbiosis of carcinogenesis, we assessed alterations in gut microbiota in patients with CRC. A total of 23 subjects were enrolled in this study: 9 had CRC (CRC group) and 14 had normal colons (normal group). The microbiome of the mucosal-luminal interface of each subject was sampled and analyzed using 16S rRNA gene amplicon sequencing. We also used Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict microbial functional profiles. The microbial composition of the mucosal lumen differed between the groups, and the presence of specific bacteria may serve as a potential biomarker for colorectal carcinogenesis. We identified a significant reduction in Eubacterium, which is a butyrate-producing genera of bacteria, and a significant increase in Devosia in the gut microbiota of CRC patients. Different levels of gut microflora in healthy and CRC samples were identified. The observed abundance of bacterial species belonging to Eubacterium and Devosia may serve as a promising biomarker for the early detection of CRC.

Background: A western high fat, high carbohydrate diet has been shown to be associated with decreased gut bacterial diversity and reductions in beneficial bacteria. This gut bacteria dysbiosis could develop in early life and contribute to chronic disease risk such as obesity, type 2 diabetes and non-alcoholic fatty liver disease.Objective: To determine how dietary macronutrients are associated with the relative abundance of gut bacteria in healthy adolescents.Methods: Fifty-two obese participants (12-19 years) from two studies, many who were primarily of Hispanic background, provided fecal samples for 16S rRNA gene sequencing. Dietary macronutrients were assessed using 24-hour diet recalls and body composition was assessed using DEXA. General regression models assuming a negative binomial distribution were used to examine the associations between gut bacteria and dietary fiber, saturated fat, unsaturated fats, protein, added sugar, total sugar and free fructose after adjusting for age, gender, race/ethnicity, body fat percentage, study and caloric intake.Results: The genera Eubacterium (Benjamini-Hochberg (BH) corrected p-value = 0.10) and Streptococcus (BH corrected p-value = 0.04) were inversely associated with dietary fructose intake. There were no other significant associations between abundances of gut microbes and other dietary macronutrients, including fiber, fat, protein, total sugar or added sugar.Conclusions: High dietary fructose was associated with lower abundance of the beneficial microbes Eubacterium and Streptococcus, which are involved with carbohydrate metabolism.

The thioredoxin system is a ubiquitous oxidoreductase system that consists of the enzyme thioredoxin reductase (TrxR), its cofactor nicotinamide adenine dinucleotide phosphate (NAD(P)H) and the protein thioredoxin (Trx). The system has been comprehensively studied from many organisms, such as Escherichia coli (E. coli); however, structural and functional analysis of this system from thermophilic bacteria has not been as extensive. In this study, Thermosipho africanus, a thermophilic eubacterium, Trx1 (TaTrx1) was successfully cloned, overexpressed and purified, to greater than 95% purity. Inspection of the amino acid sequence of TaTrx1 categorized the protein as a putative Trx. Its ability to reduce the interchain disulfides of insulin, in the presence of dithiothreitol, provided further evidence to suggest that it was a Trx. The three dimensional structure of the protein, determined using X-ray crystallography, provided additional evidence for this. The crystal structure was solved in space group P212121 to 1.8 Ă resolution and showed the characteristic thioredoxin fold; four β-strands surrounded by three α-helices. The active site of TaTrx1 contained two cysteines that formed a disulfide bridge, and was structurally similar to the active site of EcTrx1. Further studies indicated that TaTrx1 was far more stable than Trx1 of E. coli (EcTrx1). The protein could withstand both higher temperatures and higher concentrations of guanidine hydrochloride before denaturing. Our studies have therefore identified a novel thermophilic putative Trx that structurally and functionally behaves like a Trx.

The extremely thermophilic eubacterium Fervidobacterium islandicum AW-1 produces low molecular weight (LMW; < 1 kDa) keratin peptides (KPs) from poultry feathers at 70°C. However, detection and quantification of feather hydrolysate-derived peptides is needed for optimizing fermentation and down-stream processes. Herein, we developed a large-scale fermentation and purification of skin anti-aging LMW KPs from recalcitrant feathers using fluorescence-based quantification of N-terminal prolinecontaining KPs derivatized with 3,4-dihydroxybenzoic acid to yield fluorescent adducts. Fluorescent products were correlated with bioactive KP concentrations in keratin fractions and cosmetic formulations. Subsequent anaerobic fermentative keratinolysis and large-scale purification achieved 4.4 g/L LMW KPs from 8 g/L native feathers in a 5 L batch bioreactor, generating 0.8 g/L purified MMP-1 suppressive KPs (yield = 1.2%). This demonstrated the feasibility of industrial-scale anaerobic feather digestion and purification of LMW KPs to produce skin anti-aging peptides from keratin hydrolysates in a more environmentally sustainable manner.

Ingestion of silver nanoparticles (AgNPs) is inevitable linked to their widespread use in food, medicines and other consumer products. However, their effects on human microbiota at non-lethal concentrations remain poorly understood. In this study, the interactions among 1 μg mL−1 AgNPs, the intestinal microbiota, and the probiotic Bacillus subtilis (BS) were tested using in-vitro batch fermentation models inoculated with human fecal matter. Results from metagenomic investigations revealed that the core bacterial community was not affected by the exposure of AgNPs and BS at the later stage of fermentation, while the proportions of rare species changed drastically with the treatments. Furthermore, shifts in the Firmicutes/Bacteriodetes (F/B) ratios were observed after 24 h with an increase in the relative abundance of Firmicutes species and a decrease in Bacteroidetes in all fermentation cultures. The co-exposure to AgNPs and BS led to the lowest F/B ratio. Fluorescent in-situ hybridization analyses indicated that non-lethal concentration of AgNPs negatively affected the relative percentage of Faecalibacterium prausnitzii and Clostridium coccoides/Eubacterium rectales taxa in the fermentation cultures after 24 h. However, exposure to single and combined treatments of AgNPs and BS did not change the overall diversity of the fecal microflora. Functional differences in cell motility, translation, transport, and xenobiotics degradation occurred in AgNPs-treated fermentation cultures but not in AgNPs+BS-treated samples. Compared to the control samples, treated fecal cultures showed no significant statistical differences in terms of short-chain fatty acids profiles, cytotoxic and genotoxic effects on Caco-2 cell monolayers. Overall, AgNPs did not affect the composition and diversity of the core fecal microflora and its metabolic and toxic profiles. This work indicated a chemopreventive role of probiotic on fecal microflora against AgNPs, which were shown by the decrease of F/B ratio and the unaltered state of some key metabolic pathways.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by impairments in social interactions and communication, restricted interests and repetitive behaviors. Several studies report a high prevalence of gastrointestinal (GI) symptoms in autistic individuals. Cumulative evidence reveals that the gut microbiota and its metabolites (especially short-chain fatty acids, SCFAs) play an important role in GI disorders and the pathogenesis of ASD. However, the composition of the gut microbiota and its association with fecal SCFAs and GI symptoms of autistic children remain largely unknown. In the present study, we sequenced the bacterial 16S rRNA gene, detected fecal SCFAs, assessed GI symptoms and analyzed the relationship between the gut microbiome and fecal SCFAs in autistic and neurotypical individuals. The results showed that the compositions of the gut microbiota and SCFAs were altered in ASD individuals. We found lower levels of fecal acetic acid and butyrate and a higher level of fecal valeric acid in ASD subjects. We identified decreased abundances of key butyrate-producing taxa (Ruminococcaceae, Eubacterium, Lachnospiraceae and Erysipelotrichaceae) and an increased abundance of valeric acid associated bacteria (Acidobacteria) among autistic individuals. Constipation was the only GI disorder in ASD children in the present study. We also found enriched Fusobacterium, Barnesiella, Coprobacter and valeric acid-associated bacteria (Actinomycetaceae) and reduced butyrate-producing taxa in constipated autistic subjects. It is suggested that the gut microbiota contributes to fecal SCFAs and constipation in autism. Modulating the gut microbiota, especially butyrate-producing bacteria, could be a promising strategy in the search for alternatives for the treatment of autism spectrum disorder.

Irinotecan (CPT-11), a first-line chemotherapy for advanced colorectal cancer, causes serious diarrhea in patients receiving treatment. The underlying mechanism has been shown that the active metabolite of CPT-11, SN-38, is metabolized to the inactive metabolite SN-38 glucuronide (SN-38 G) during hepatic glucuronidation, and subsequently is exported into the intestine, where SN-38 G is hydrolyzed by bacterial β-glucuronidase (βG) to be SN-38, thus leading to intestinal toxicity. Thus, inhibition of the intestinal bacterial βG activity is expected to prevent CPT-11-induced diarrhea. However, the effects of such inhibition on serum pharmacokinetics of SN-38, the key determinant of CPT-11 treatment, are uncertain. Here, we determined the effects of a potent E. coli βG (eβG)-specific inhibitor pyrazolo[4,3-c]quinoline derivative (TCH-3562) for the potential use in preventing CPT-11-induced diarrhea. TCH-3562 exhibited efficacious inhibitory potency of endogenous βG activity in two anaerobes, Eubacteriumsp. and Peptostreptococcus anaerobius. Oral administration of TCH-3562 also effectively reduced the bacterial βG activity in mice intestine. Moreover, pharmacokinetic analysis of TCH-3562 revealed a relatively low amount of TCH-3562 was detected in the plasma whereas the majority of TCH-3562 was found in the feces. Importantly, co-treatment of CPT-11 and TCH-3562 did not decrease active SN-38 level in mice plasma. Finally, we established that TCH-3562 as an adjuvant treatment showed protective effects on CPT-11-induced diarrhea and had no negative effects on the therapeutic efficacy of CPT-11 in tumor-bearing mice. Therefore, inhibition of the intestinal bacterial βG activity by the specific inhibitor, TCH-3562, is promising to prevent CPT-11-induced diarrhea while maintaining its anti-tumor efficacy that may have clinical potentials for the treatment with CPT-11.

No microbiological criteria were included in the 2018 EFP-AAP classification of periodontal diseases that could be used to differentiate between stages and grades. Furthermore, differences in the subgingival microbiome depending on stage and grade have not been established. Sixty subgingival biofilm samples were collected in Spain (n = 30) and Colombia (n = 30) from three distinct patient categories: those with periodontal health/gingivitis (n = 20), those with stage I-II periodontitis (n = 20), and those with stage III-IV periodontitis (n = 20). Patients were evaluated by 16S rRNA gene amplification sequencing. Amplicon sequence variants were used to assign taxonomic categories compared to the Human Oral Microbiome Database (threshold ≥97% identity). Alpha diversity was established by Shannon and Simpson indices, and principal coordinate analysis, ANOSIM, and PERMANOVA of the UNIFRAC distances were performed using QIIME2. Although differences in the alpha diversity were observed between samples according to country, Filifactor alocis, Peptostreptococcaceae [XI][G-4] bacterium HMT 369, Fretibacterium fastidiosum, Lachnospiraceae [G-8] bacterium HMT 500, Peptostreptococcaceae [XI][G-5] [Eubacterium] saphenum, Peptostreptococcus stomatis, and Tannerella forsythia were associated with periodontitis sites in all stages. However, only F. alocis, Peptostreptococcaceae [XI][G-4] bacterium HMT 369, Peptostreptococcaceae [XI][G-9] [Eubacterium] brachy, Peptostreptococcaceae [XI][G-5] [Eubacterium] saphenum, and Desulfobulbus sp. HMT 041 were consistent in stage III-IV periodontitis in both countries. Porphyromonas gingivalis and Tannerella forsythia were differentially expressed in severe lesions in the countries studied. Although some non-cultivable microorganisms showed differential patterns between the different stages of periodontitis, they were not the same in the two countries evaluated. Further studies using larger samples with advanced next-generation techniques for high-throughput sequencing of phyla and non-cultivable bacteria within the subgingival microbiome could provide more insight into the differences between stages of periodontitis.

Microbiota-induced tumorigenesis is well established in solid tumors of the gastrointestinal tract but rarely explored in hematologic malignancies. To determine the role of gut microbiota in lymphoma progression, we performed metagenomic sequencing on human primary gastrointestinal B cell lymphomas. We identified a distinct microbiota profile of intestinal lymphoma, with significantly decreased symbiotic microbes, particularly the genus Eubacterium and notably butyrate-producing Eubacterium rectale. Transfer of E. rectale-deficit microbiota of intestinal lymphoma patients to mice caused inflammation and tumor necrosis factor (TNF) production. Conversely, E. rectale treatment reduced TNF levels and the incidence of lymphoma in sensitized Eμ-Myc mice. Moreover, lipopolysaccharide from the resident microbiota of lymphoma patients and mice synergizes with TNF signaling and reinforces the NF-κB pathway via the MyD88-dependent TLR4 signaling, amalgamating in enhanced intestinal B cell survival and proliferation. These findings reveal a mechanism of inflammation-associated lymphomagenesis and a potential clinical rationale for therapeutic targeting of gut microbiota.

As an important part of ecosystem, microbes are widely distributed in various habitats. In recent years, more and more attention has been paid to the study on gut microbiota. The gut microbiota and their metabolites influence human and animal nutrition processing, metabolic balance, immune function, gastrointestinal development and other physiological activities. With the deepening of studies on human and animal gut microbiota, it has been found that some factors, such as diet, age, gender, and living environment, impacting on the composition of gut microbiota, while the differences among animal species have more significant influence on the gut microbiota composition. In relatively primitive grassland ecosystems, soil microbes interact with human and animal activities. On the one hand, microbes in the soil environment are the driving forces for the transformation and circulation of organic matter and nutrients. The improvement of soil microbial community diversity is beneficial for the soil fertility. On the other hand, human and animal activities will affect the diversity of soil microbial community. Although there are a lot of researches on soil microbiota, animal and human gut microbiota, their differences in diversity and composition within the same environment have not been studied. The advent of sequencing technology provides an effective mean for the accurate and comprehensive understanding of microbes, especially for the study of uncultivable microorganisms. The PacBio single-molecule real-time (SMRT) technology is advantageous in producing long sequence reads with high accuracy. Based on sequencing the full length 16S rRNA genes, the microbiota composition can be identified to the species level. Therefore, it is an effective approach for studying microbial diversity. We collected 56 stool and soil samples from Xilinguole, including 6, 10, 11, 9, and 10 stool samples from human, goat, cattle, horse, and sheep, respectively, as well as 10 soil samples. Genomic DNA was extracted from the samples. After DNA extraction and quality check, the 16S rRNA genes of all samples were amplified from the genomic DNA. The PCR products were sequenced using the PacBio RS II instrument. The QIIME software (V1.7) was used to analyze the sequencing data, and the R software (version 3.5.0) was used to further analyze and visualize the results. Firstly, it was found that the gut microbiota diversity of human was significantly lower than other samples ( P 0.01). The overall composition of the human and animal gut microbiota were dominated by the Firmicutes and Bacteroidetes phyla. However, the soil microbiota was dominated by Proteobacteria and Acidobacteria. At the genus level, the sheep, goat and cattle gut microbiota were dominated by Clostridium , Bacteroides , and Oscillibacter , while the horse gut microbiota was mainly composed of Clostridium , Eubacterium , and Treponema . The soil microbiota was composed mainly of Blastocatella and Bacillus . The human gut microbiota comprised much of Veillonella , Clostridium , Escherichia/Shigella . At the species level, the human gut microbiota mainly contained Escherichia/Shigella , dysenteriae , Streptococcus salivarius . The sheep, goat, cattle, and horse gut microbiota were dominated by Oscillibacter valericigenes and Eubacterium coprostanoligenes . The major species in soil were Blastocatella fastidiosa and Bacillus longiquaesitum . Moreover, principal coordinate analysis (PCoA) and hierarchical clustering analysis showed some differences in the microbiota structure among human gut, animal gut and soil samples. The gut microbiota structure was similar among cattle, goats and sheep. They were more different from the samples collected from human, horse and soil. We classified all samples into four clusters. Cluster 1 only included human samples; cluster 2 comprised the horse samples; cluster 3 was consisted of the sheep, goat, and cattle samples; while cluster 4 contained only the soil samples. Lastly, we identified the discriminatory OTUs and assigned them taxonomically to the species level. In conclusion, there were significant differences between animal gut microbiota and soil microbiota. The soil microbiota was more complex. As an omnivore, human gut microbiota diversity was significantly lower than other herbivorous animal (namely cattle, goat, horse and sheep). Although cattle, sheep, goat and horses are all herbivorous animals, the distinct features of the digestive systems could contribute to the difference in gut microbiota composition of horse from those of sheep, goat and cattle. This study revealed the differences of gut microbiota diversity between human and other animals, as well as from the soil microbial community. This work has laid a theoretical foundation for further studies on microbial diversity in different habitats.

Peroxiredoxins (Prxs) are thiol peroxidases that scavenge various peroxide substrates such as hydrogen peroxide (H2O2), alkyl hydroperoxides and peroxinitrite. They also function as chaperones and are involved in signal transduction by H2O2 in eukaryotic cells. The genome of Aquifex aeolicus, a microaerophilic, hyperthermophilic eubacterium, encodes four Prxs, among them an alkyl hydroperoxide reductase AhpC2 which was found to be closely related to archaeal 1-Cys peroxiredoxins. We determined the crystal structure of AhpC2 at 1.8 A resolution and investigated its oligomeric state in solution by electron microscopy. AhpC2 is arranged as a toroid-shaped dodecamer instead of the typically observed decamer. The basic folding topology and the active site structure are conserved and possess a high structural similarity to other 1-Cys Prxs. However, the C-terminal region adopts an opposite orientation. AhpC2 contains three cysteines, Cys49, Cys212, and Cys218. The peroxidatic cysteine CP49 was found to be hyperoxidized to the sulfonic acid ( SO3H) form, while Cys212 forms an intra-monomer disulfide bond with Cys218. Mutagenesis experiments indicate that Cys212 and Cys218 play important roles in the oligomerization of AhpC2. Based on these structural characteristics, we proposed the catalytic mechanism of AhpC2. This study provides novel insights into the structure and reaction mechanism of 1-Cys peroxiredoxins.

The objective of this study was to observe the effects of anthocyanin from purple corn on blood biochemical indexes, ruminal fluid fermentation parameters, and the microbial population in goats. A total of 18 Qianbei Ma wether kids (body weight, 21.38 ± 1.61 kg; mean ± standard deviation) were randomly assigned to three groups using a completely randomized design. The group diets were: (1) control, basal diet, (2) treatment 1 (LA), basal diet with 0.5-g/d purple corn pigment (PCP), and (3) treatment 2 (HA), basal diet with 1-g/d PCP. The results showed that supplementation of PCP anthocyanin increased (P < 0.05) crude protein and gross energy digestibilities compared to the control. Compared to the control group, the inclusion of anthocyanin-rich PCP led to significantly increased (P < 0.05) plasma reduced glutathione and peroxidase concentrations. Goats receiving PCP had increased (P < 0.05) ruminal fluid acetic acid and a higher ratio of acetate to propionate, while the propionic acid, butyric acid, valeric acid, isobutyric acid, and isovaleric acid levels had decreased (P < 0.05). There was no significant difference (P > 0.05) in ruminal fluid alpha bacterial diversity among the three groups. At the phylum level, the feeding of PCP had significant effect (P < 0.05) on the abundances of Actinobacteriota, Proteobacteria, Elusimicrobiota, WPS-2, and Cyanobacteria. At the genus level, HA group had lower (P < 0.05) Prevotellaceae_NK3B31_group abundance compared to the other groups. In addition, significant differences (P < 0.05) were also observed for the ruminal fluid Eubacterium_nodatum_group, Amnipila, Ruminiclostridium, U29-B03, unclassified_c_Clostridia, Pyramidobacter, Anaeroplasma, UCG-004, Atopobium, norank_f_norank_o_Bradymonadales, Elusimicrobium, norank_f_norank_o_norank_c_norank_p_WPS-2, norank_f_Bacteroidales_UCG-001, and norank_f_norank_o_Gastranaerophilales among all groups. Taken together, the inclusion of anthocyanin-rich PCP increased the antioxidant potential, improved rumen volatile fatty acids, and induced a shift in the structure and relative abundance of ruminal microbiota in growing goats.

A vegan diet could impact microbiota composition and bacterial metabolites like short-chain (SCFA) and branched-chain fatty acids (BCFA). The aim of this study was to compare the concentrations of SCFA, BCFA, ammonia, and fecal pH between vegans and omnivores. In this cross-sectional study (vegans n = 36, omnivores n = 36), microbiota composition, fecal SCFA, BCFA, and ammonia concentrations and pH were analyzed in complete stool samples. A random forest regression (RFR) was used to identify bacteria predicting SCFA/BCFA concentrations in vegans and omnivores. No significant differences in SCFA and BCFA concentrations were observed between vegans and omnivores. Fecal pH (p = 0.005) and ammonia concentration (p = 0.01) were significantly lower in vegans than in omnivores, while fiber intake was higher (p &lt, 0.0001). Shannon diversity was higher in omnivores compared to vegans on species level (p = 0.04) only. In vegans, a cluster of Faecalibacterium prausnitzii, Prevotella copri, Dialister spp., and Eubacterium spp. was predictive for SCFA and BCFA concentrations. In omnivores, Bacteroides spp., Clostridium spp., Ruminococcus spp., and Prevotella copri were predictive. Though SCFA and BCFA did not differ between vegans and omnivores, the results of the RFR suggest that bacterial functionality may be adapted to varying nutrient availability in these diets.

One of the bottlenecks of the hydrogen production by dark fermentation is the low yields obtained because of the homoacetogenesis persistence, a metabolic pathway where H2 and CO2 are consumed to produce acetate. The central reactions of H2 production and homoacetogenesis are catalyzed by enzyme hydrogenase and the formyltetrahydrofolate synthetase, respectively. In this work, genes encoding for the formyltetrahydrofolate synthetase (fthfs) and hydrogenase (hydA) were used to investigate the diversity of homoacetogens as well as their phylogenetic relationships through quantitative PCR (qPCR) and next-generation amplicon sequencing. A total of 70 samples from 19 different H2-producing bioreactors with different configurations and operating conditions were analyzed. Quantification through qPCR showed that the abundance of fthfs and hydA was strongly associated with the type of substrate, organic loading rate, and H2 production performance. In particular, fthfs sequencing revealed that homoacetogens diversity was low with one or two dominant homoacetogens in each sample. Clostridium carboxivorans was detected in the reactors fed with agave hydrolisates; Acetobacterium woodii dominated in systems fed with glucose; Blautia coccoides and unclassified Sporoanaerobacter species were present in reactors fed with cheese whey; finally, Eubacterium limosum and Selenomonas sp. were co-dominant in reactors fed with glycerol. Altogether, quantification and sequencing analysis revealed that the occurrence of homoacetogenesis could take place due to (1) metabolic changes of H2-producing bacteria towards homoacetogenesis or (2) the displacement of H2-producing bacteria by homoacetogens. Overall, it was demonstrated that the fthfs gene was a suitable marker to investigate homoacetogens in H2-producing reactors. • qPCR and sequencing analysis revealed two homoacetogenesis phenomena. • fthfs gene was a suitable marker to investigate homoacetogens in H2 reactors.

Methanol is the simplest of all alcohols, is universally distributed in anoxic sediments as a result of plant material decomposition and is constantly attracting attention as an interesting substrate for anaerobes like acetogens that can convert bio-renewable methanol into value-added chemicals. A major drawback in the development of environmentally friendly but economically attractive biotechnological processes is the present lack of information on biochemistry and bioenergetics during methanol conversion in these bacteria. The mesophilic acetogen Eubacterium callanderi KIST612 is naturally able to consume methanol and produce acetate as well as butyrate. To grasp the full potential of methanol-based production of chemicals, we analysed the genes and enzymes involved in methanol conversion to acetate and identified the redox carriers involved. We will display a complete model for methanol-derived acetogenesis and butyrogenesis in Eubacterium callanderi KIST612, tracing the electron transfer routes and shed light on the bioenergetics during the process.

Recently, aging is considered a risk factor for various diseases. Although changes in the intestinal microbiota along with aging are thought to associate with the increased disease risk, mechanisms that cause age-related transition of the intestinal microbiota remain unknown. This study aims to clarify relationships between the amount of human defensin 5 (HD5), a Paneth cell α-defensin, which is known to regulate the intestinal microbiota, and age-related differences of the intestinal microbiota composition. Fecal samples from 196 healthy Japanese (35 to 81 years old) were collected and measured HD5 concentration. HD5 concentration in the elderly group (age > 70 years old) was significantly lower than the middle-aged group (age ≤ 70 years old). Furthermore, individual age was negatively correlated with HD5 concentration (r = − 0.307, p Collinsella, Alistipes, Peptococcaceae; unassigned, Lactobacillus, Lactococcus, Weissella, Christensenellaceae R-7 group, Megasphaera, and [Eubacterium] eligens group was significantly higher, and Lachnospiraceae; unassigned, Blautia, Anaerostipes, Fusicatenibacter, Dorea, and Faecalibacterium was significantly lower in the elderly compared to the middle-aged. In addition, HD5 concentration was negatively correlated with Alistipes, Peptococcaceae; unassigned, and Christensenellaceae R-7 group and positively correlated with Lachnospiraceae; unassigned and Dorea. These results provide novel insights into the immunosenescence of enteric innate immunity, indicating low HD5 is suggested to contribute to the age-related differences in the intestinal microbiota and may relate to increased risk of diseases in elderly people.

To compare the effects of three mannans, Konjac glucomannan (KGM), guar gum (GG) and locust bean gum (LBG), on obesity and obesity-related metabolic disorders in mice fed with high-fat diet (HFD), and to investigate the potential modulation of gut microbiota, we performed a 14 week study on C57BL/6J mice fed a HFD with/without mannan supplementation. The results showed that supplementing 8% KGM, GG, and LBG to a HFD dramatically reduced the body weight gain and adipose accumulation, attenuated liver injury, and antagonized glycolipid metabolism and inflammation-related parameters of HFD-fed mice in different degrees. However, only LBG had such roles when the supplement dose was reduced to 2%. In addition, it was found that LBG required more time to exert its impacts on weight control and lipid metabolism. Furthermore, 16S rRNA gene sequencing of gut microbiota indicated that mannans with different structures and supplement doses affected the overall structure of the gut microbiota to a varying extent and specifically changed the abundance of some OTUs. Moreover, several OTUs belonging to the genera Muribaculum, Staphylococcus, [Eubacterium] fissicatena group, and Christensenella had a high correlation with obesity and obesity-related metabolic disorders of the host. In summary, all the three mannans had the potential to be used as alternative dietary supplements or functional foods to prevent obesity and obesity-related metabolic disorders induced by a HFD, but the effects of the dose and time varied, and the functions of the mannans were associated with their ability to regulate the gut microbiota.

Size-exclusion chromatography (SEC) coupled with multiangle light scattering detection (SEC/MALS) enables determination of the molecular weight, oligomeric state, and stoichiometry of protein-nucleic acid complexes in solution. Often such complexes show anomalous behavior on SEC, thus presenting a challenge in determination of molecular weight and stoichiometry based solely on the elution position from SEC. In contrast to analytical ultracentrifugation, the SEC/MALS analysis is not affected by the shape of the complex. Here we describe the use of SEC/MALS for characterization of the stoichiometry of the complex between the reverse transcriptase (RT) domain from group II intron-maturase from Eubacterium rectale and intron RNA, and for monitoring protein dimerization that is driven by interaction between single-stranded DNA upstream of the P1 promoter, known as FUSE and FUSE binding protein-interacting repressor (FIR).

Objectives Oral microbiome plays an important role in oral diseases. Among them, proliferative verrucous leucoplakia (PVL) is an uncommon form of progressive multifocal leukoplakia with a worryingly rate of malignant transformation. Here, we aimed to characterize the oral microbiome of PVL patients and compare it with those of healthy controls. Material and methods Oral biopsies from ten PVL patients and five healthy individuals were obtained and used to compare their microbial communities. The sequence of the V3-V4 region of 16S rRNA gene was used as the taxonomic basis to estimate and analyze the composition and diversity of bacterial populations present in the samples. Results Our results show that the oral microbial composition and diversity are significantly different among PVL patients and healthy donors. The average number of observed operational taxonomic units (OTUs) was higher for healthy donors than for PVL, proving a loss of diversity in PVL. Several OTUs were found to be more abundant in either group. Among those that were significantly enriched in PVL patients, potential protumorigenic pathogens like Oribacterium sp. oral taxon 108, Campylobacter jejuni, uncultured Eubacterium sp., Tannerella, and Porphyromonas were identified. Conclusion Oral microbiome dysbiosis was found in patients suffering from PVL. To the best of our knowledge, this is the first study investigating the oral microbiome alterations in PVL and, due to the limited number of participants, additional studies are needed. Oral microbiota-based biomarkers may be helpful in predicting the risks for the development of PVL.

The human gut is a highly diverse microbial ecosystem. Although showing a well-defined core of dominant taxa, an interindividual variability exists in microbiome arrangement patterns, and the presence and proportion of specific species, determining individual metabolic features-metabotypes-which govern the health effects of dietary interventions (i.e. polyphenol consumption). Starting with a 19-volunteer human intervention study, divided into low, medium, and high wine-polyphenol-metabolizers, we detected interindividual discrepancies on the effect of wine consumption in gut bacterial alpha-diversity, but a significant homogenization of beta-diversity among moderate wine consumers, independently of their metabotype. In addition, the abundance of key health-related taxa such as Akkermansia sp. increased after moderate wine intake in the group of high polyphenol-metabolizers. Regarding the metabolic activity, significant (p < 0.05) positive correlations in the production of SCFAs were observed after wine intake. Finally, we were able to correlate the microbiome and the metabolome of the three metabotypes, and to identify some metabolites-biomarker species, highlighting the genera Phascolarctobacterium, Pelotomaculum and Prevotella, as positively correlated with polyphenol concentration, and Prevotella, Zymophilus and Eubacterium as positively correlated with SCFAs concentration in faeces. Our results contribute to the evidence of the need of including the microbiome variable in personalized nutrition programs, as different metabotyes respond differently to dietary interventions., This work has been carried out within the framework of the URJC's “WINE MICROBIAL ECOLOGY AND BIOTECHNOLOGY” unit with CSIC. Research in our labs is funded by Grants AGL2015-64522-C2-R, PID2019-108851RB-C21 and PID2019-105834GA-I00 (Spanish Ministry of Science and Innovation), and ALIBIRD-CM 2020 P2018/BAA-4343 (Comunidad de Madrid, Spain).

Growing evidence highlights the crucial role of gut microbiota in affecting different aspects of obesity. Considering the ability of deep transcranial magnetic stimulation (dTMS) to modulate the cortical excitability, the reward system, and, indirectly, the autonomic nervous system (ANS), we hypothesized a potential role of dTMS in affecting the brain-gut communication pathways, and the gut microbiota composition in obesity. In a hospital setting, 22 subjects with obesity (5 M, 17 F, 44.9 ± 2.2 years, BMI 37.5 ± 1.0 kg/m2) were randomized into three groups receiving 15 sessions (3 per week for 5 weeks) of high frequency (HF), low frequency (LF) dTMS, or sham stimulation. Fecal samples were collected at baseline and after 5 weeks of treatment. Total bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool Mini Kit (Qiagen, Italy) and analyzed by a metagenomics approach (Ion Torrent Personal Genome Machine). After 5 weeks, a significant weight loss was found in HF (HF: −4.1 ± 0.8%, LF: −1.9 ± 0.8%, sham: −1.3 ± 0.6%, p = 0.042) compared to LF and sham groups, associated with a decrease in norepinephrine compared to baseline (HF: −61.5 ± 15.2%, p &lt, 0.01, LF: −31.8 ± 17.1%, p &lt, 0.05, sham: −35.8 ± 21.0%, p &gt, 0.05). Furthermore, an increase in Faecalibacterium (+154.3% vs. baseline, p &lt, 0.05) and Alistipes (+153.4% vs. baseline, p &lt, 0.05) genera, and a significant decrease in Lactobacillus (−77.1% vs. baseline, p &lt, 0.05) were found in HF. Faecalibacterium variations were not significant compared to baseline in the other two groups (LF: +106.6%, sham: +27.6%, p &gt, 0.05) as well as Alistipes (LF: −54.9%, sham: −15.1%, 0.05) and Lactobacillus (LF: −26.0%, sham: +228.3%, 0.05) variations. Norepinephrine change significantly correlated with Bacteroides (r2 = 0.734, p &lt, 0.05), Eubacterium (r2 = 0.734, 0.05), and Parasutterella (r2 = 0.618, 0.05) abundance variations in HF. In conclusion, HF dTMS treatment revealed to be effective in modulating gut microbiota composition in subjects with obesity, reversing obesity-associated microbiota variations, and promoting bacterial species representative of healthy subjects with anti-inflammatory properties.

Background Colonization of intestinal microbiota in ruminant during the early life is important to host health, metabolism and immunity. Accumulating evidence revealed the ameliorative effect of milk replacer administration in the gut microbial development of early-weaned ruminants. Yimeng black goats (YBGs) inhabiting Shandong, China show a complex intestinal microbial ecosystem, but studies of their gut microbiota are still insufficient to report. Here, this study was performed to investigate how the gut microbiota develops in weaned YBGs with the effect of age and milk replacer. Results Results indicated that both age and milk replacer were important factors to change the gut microbiota of YBGs. Although the alpha diversity of gut microbiota did not change with the age of YBGs, the taxonomic compositions significantly changed. The relative abundance of some beneficial bacteria such as Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Eubacterium and Barnesiella significantly decreased and subsequently increase with age, which contributes to maintain the stability of intestinal environment and realize the diversity of intestinal functions. The relative abundance of Porphyromonas, Brevundimonas, Flavobacterium, Stenotrophomonas, Propionibacterium, Acinetobacter, Enterococcus and Clostridium belong to pathogenic bacteria in milk replacer-treated YBGs was significantly decreased. Additionally, some beneficial bacteria such as Ruminococcus, Ruminococcaceae, Christensenellaceae and Ruminiclostridium also display a trend of decreasing first followed by gradually increasing. Conclusions This study first revealed the gut bacterial community alterations in YBGs with the effect of age and milk replacer. This study also characterized the gut microbial distribution in YBGs with different ages and provided better insight into microbial population structure and diversity of YBGs. Moreover, milk replacer may serve as a good applicant for improving gut microbial development in early-weaned YBGs.

The intestinal fermentability of pectic polysaccharides is largely determined by its molecular size. In this study, fermentation properties of enzymatic-modified apple pectin (AP) and homogalacturonans (HG) with high, medium and low molecular weight (Mw) were evaluated by in vitro fermentation model, and their structural changes were also investigated. Results showed that Mw, monosaccharide contents and molecular linearity of the AP hydrolysates were reduced after microbial degradation. On the other hand, culture media supplemented with low-Mw AP (60,300 g/mol) and low-Mw HG (861 g/mol) exhibited lower pH (5.1 and 5.7, respectively) and produced higher total short-chain fatty acid contents (SCFA, 230.40 mmol/L and 187.19 mmol/L, respectively). However, reduced trends in abundance of the pectinolytic microorganisms Faecalibacterium and Eubacterium were showed as Mw of the HG decreased, whereas growth of the SCFA-producer genera Bifidobaacterium, Megasphaera and Allisonella were improved. This work confirmed that low-Mw pectin and homogalacturonan generated more beneficial metabolites, developing structure-microbiota-gut health relationship.

This study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), n = 4), or sterilized rumen content (Con, n = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing. Abomasum tissues were collected immediately after sacrifice at 8 weeks of age. Five genera (Tannerella, Desulfovibrio, Deinococcus, Leptotrichia, and Eubacterium, P &lt, 0.05) showed significant difference in abundance between the treatments. A total of 975 differentially expressed genes were identified (P &lt, 0.05, fold-change &gt, 1.5, mean read-counts &gt, 5). Pathway analysis indicated that up-regulated genes were involved in immune system process and defense response to virus, while the down-regulated genes involved in ion transport, ATP biosynthetic process, and mitochondrial electron transport. Positive correlation (r &gt, 0.7, P &lt, 0.05) was observed between TRPM4 gene and Desulfovibrio, which was significantly higher in the HE group. TRPM4 had a reported role in the immune system process. In conclusion, the dosing of adult rumen contents to calves can alter not only the composition of active microorganisms in the abomasum but also the molecular mechanisms in the abomasum tissue, including reduced protease secretion and decreased hydrochloric acid secretion.

Rheumatic heart disease refers to the long-term damage of heart valves and results from an autoimmune response to group A Streptococcus infection. This study aimed to analyze the microbiota composition of patients with rheumatic heart disease and explore potential function of microbiota in this disease. First, we revealed significant alterations of microbiota in feces, subgingival plaques, and saliva of the patients compared to control subjects using 16S rRNA gene sequencing. Significantly different microbial diversity was observed in all three types of samples between the patients and control subjects. In the gut, the patients possessed higher levels of genera including Bifidobacterium and Eubacterium, and lower levels of genera including Lachnospira, Bacteroides, and Faecalibacterium. Coprococcus was identified as a super-generalist in fecal samples of the patients. Significant alterations were also observed in microbiota of subgingival plaques and saliva of the patients compared to control subjects. Second, we analyzed microbiota in mitral valves of the patients and identified microbes that could potentially transmit from the gut or oral cavity to heart valves, including Streptococcus. Third, we further analyzed the data using random forest model and demonstrated that microbiota in the gut, subgingival plaque or saliva could distinguish the patients from control subjects. Finally, we identified gut/oral microbes that significantly correlated with clinical indices of rheumatic heart disease. In conclusion, patients with rheumatic heart disease manifested important alterations in microbiota that might distinguish the patients from control subjects and correlated with severity of this disease.

The caecum is the primary site where microbial fermentation and acidosis occurred. The supplementation of starter feed and alfalfa hay has the potential to influence caecal microbiota and then affect caecal fermentation. This study aims to investigate the effect of starter feed and alfalfa hay supplementation on caecal microbiota, immune homeostasis, and growth of preweaning yaks. Twenty 30-day-old male yak calves were randomly assigned to four groups, which separately fed with milk replacer (CON group), milk replacer with alfalfa hay (A group), milk replacer with starter feed (S group), and milk replacer with starter feed plus alfalfa hay (SA group) throughout the trial. Growth performance and plasma physiological and biochemical indicators were measured every 30 days. Calves were sacrificed at 120 days of age. The caecal contents were collected for measuring pH and contents of volatile fatty acids (VFAs) and lipopolysaccharide (LPS) and for characterizing caecal microbiota. The results indicated that individual or simultaneous supplementation with alfalfa hay and starter feed all significantly increased the BW, body height, body length, and chest girth of yak calves. However, supplementation with starter feed significantly increased plasma cortisol, nitric oxide, tumor necrosis factor-α, and interferon-γ concentrations and the ratio of aspartate aminotransferase to alanine aminotransferase of yak calves when compared with the control and alfalfa hay feeding groups, while the co-supplementation of starter feed and alfalfa hay could significantly decrease these inflammation-related indices when compared with the starter feeding group. Sequencing of the 16S rRNA gene showed that starter feed and alfalfa hay separately stimulated the proliferation of starch-decomposing and cellulose- or hemicellulose-decomposing bacteria. This also significantly increased the levels of acetate, propionate, butyrate, valerate, isobutyrate, and isovalerate in the caecal contents. Furthermore, compared with the S and CON groups, the significantly increased genera of Desulfobulbus, Olsenella, Pseudoflavonifractor, and Stomatobaculum in the SA and A groups were beneficial to the immune homeostasis, and the significantly decreased Blautia, Clostridium IV, Bacteroides, Eubacterium, Clostridium XVIII, and Mogibacterium in the SA and A groups were related to the reduced caecal lactate and LPS contents, the decreased inflammatory reaction, and the improved healthy hepatic condition of yak calves. In conclusion, milk replacer supplemented with alfalfa hay and starter feed is recommended during preweaning to improve yak calf health and growth because this regimen promotes the growth and maintains the immune homeostasis of yak calves.

Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p &lt, 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p &lt, 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p &lt, 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p &lt, 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig’s phenotypic performance and nutrient metabolism.

BACKGROUND AND AIM Gut microbiota composition is associated with the pathogenesis of non-alcoholic fatty liver disease. However, the association between gut microbiota composition and non-alcoholic fatty liver disease in non-obese patients remains unclear. We compared clinical parameters and gut microbiota profiles of healthy controls and non-obese and obese patients with non-alcoholic fatty liver disease. METHODS We examined the clinical parameters and gut microbiota profiles by 16S rRNA sequences and short-chain fatty acid levels in fecal samples from 51 non-obese patients with non-alcoholic fatty liver disease (body mass index

Summary Eubacterium limosum KIST612 is one of the few acetogenic bacteria that has the genes encoding for butyrate synthesis from acetyl‐CoA, and indeed, E. limosum KIST612 is known to produce butyrate from CO but not from H2 + CO2. Butyrate production from CO was only seen in bioreactors with cell recycling or in batch cultures with addition of acetate. Here, we present detailed study on growth of E. limosum KIST612 on different carbon and energy sources with the goal, to find other substrates that lead to butyrate formation. Batch fermentations in serum bottles revealed that acetate was the major product under all conditions investigated. Butyrate formation from the C1 compounds carbon dioxide and hydrogen, carbon monoxide or formate was not observed. However, growth on glucose led to butyrate formation, but only in the stationary growth phase. A maximum of 4.3 mM butyrate was observed, corresponding to a butyrate:glucose ratio of 0.21:1 and a butyrate:acetate ratio of 0.14:1. Interestingly, growth on the C1 substrate methanol also led to butyrate formation in the stationary growth phase with a butyrate:methanol ratio of 0.17:1 and a butyrate:acetate ratio of 0.33:1. Since methanol can be produced chemically from carbon dioxide, this offers the possibility for a combined chemical‐biochemical production of butyrate from H2 + CO2 using this acetogenic biocatalyst. With the advent of genetic methods in acetogens, butanol production from methanol maybe possible as well., In this study, we have investigated the growth of and product formation by the acetogen Eubacterium limosum KIST612 on different carbon and energy sources with the goal to find substrates that lead to formation of butyrate. Butyrate is an important product that can be further reduced to the highly valuable biofuel butanol in a two‐step enzymatic process.

16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium—known butyrate producers—were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.

Background Interest in the use of natural feed additives as an alternative to antimicrobials in the poultry industry has increased in recent years because of the risk of bacterial resistance. One of the most studied groups are polyphenolic compounds, given their advantages over other types of additives and their easy potentiation of effects when complexes are formed with metal ions. Therefore, the objective of the present study was to evaluate the impact of dietary supplementation of copper acetate (CA), curcumin (CR), and their combination (CA-CR) against Salmonella Typhimurium colonization, intestinal permeability, and cecal microbiota composition in broiler chickens through a laboratory Salmonella infection model. S. Typhimurium recovery was determined on day 10 post-challenge by isolating Salmonella in homogenates of the right cecal tonsil (12 chickens per group) on Xylose Lysine Tergitol-4 (XLT-4) with novobiocin and nalidixic acid. Intestinal integrity was indirectly determined by the fluorometric measurement of fluorescein isothiocyanate dextran (FITC-d) in serum samples from blood obtained on d 10 post-S. Typhimurium challenge. Finally, microbiota analysis was performed using the content of the left caecal tonsil of 5 chickens per group by sequencing V4 region of 16S rRNA gene. Results The results showed that in two independent studies, all experimental treatments were able to significantly reduce the S. Typhimurium colonization in cecal tonsils (CT, P S. Typhimurium counts in both independent studies. Furthermore, the serum fluorescein isothiocyanate dextran (FITC-d) concentration in chickens treated with CR was significantly lower when compared to PC (P = 0.0084), which is related to a decrease in intestinal permeability and therefore intestinal integrity. The effect of dietary treatments in reducing Salmonella was further supported by the analysis of 16S rRNA gene sequences using Linear discriminant analysis effect size (LEfSe) since Salmonella was significantly enriched in PC group (LDA score > 2.0 and P Coprobacillus, Eubacterium, and Clostridium were significantly higher in the PC group compared to other treatment groups. On the contrary, Fecalibacterium and Enterococcus in CR, unknown genus of Erysipelotrichaceae at CA-CR, and unknown genus of Lachnospiraceae at CA were significantly more abundant respectively. Conclusions CR treatment was the most effective treatment to reduce S. Typhimurium intestinal colonization and maintain better intestinal homeostasis which might be achieved through modulation of cecal microbiota.

Chronic hepatitis B (CHB) is a global epidemic disease caused by hepatitis B virus that can lead to hepatic failure, even liver cirrhosis and hepatocellular carcinoma. The occurrence and development of CHB are closely related to the changes in the gut microbiota communities. To explore the relationship between the structure of gut microbiota and liver biochemical indicators, 14 CHB patients (the CHB group) and 11 healthy people (the CN group) were randomly enrolled in this study. Our results demonstrate that CHB caused changes in the gut microbiota communities and biochemical indicators, such as alanine transaminase, total bilirubin and gamma glutamyl transferase. Furthermore, CHB induced imbalance of the gut microbiota. Prevotella, Blautia, Ruminococcus, Eubacterium eligens group, Bacteroides uniformis and Ruminococcus sp. 5_1_39BFAA were associated with the critical biochemical indicators and liver injury, suggesting a new approach to CHB treatment.乙型肝炎病毒感染引起的慢性乙型肝炎 (Chronic hepatitis B，CHB) 是一种全球性流行疾病，严重时可引起肝功能衰竭，甚至发展成肝硬化和肝癌。也已发现CHB的发生和发展与肠道菌群的组成和结构的变化密切相关。为进一步探究肠道菌群结构与肝脏生化指标之间的联系，文中随机纳入14名CHB患者和11名健康对照者 (Control group，CN)，分析其肝脏生化指标和肠道菌群的结构以及两者的相关性。结果发现CHB患者肝脏生化指标丙氨酸转氨酶 (Alanine transaminase，ALT)、总胆红素 (Total bilirubin，TBIL) 和γ-谷氨酰转移酶 (Gamma glutamyl transferase，GGT) 等的水平发生显著变化；普雷沃氏菌属Prevotella、劳特氏菌属Blautia、瘤胃球菌属Ruminococcus、Eubacterium eligens group等菌属失调；单形拟杆菌Bacteroides uniformis和Ruminococcus sp. 5_1_39BFAA可能与CHB患者的肝损伤相关，提示这些菌可能成为治疗CHB的新“切入点”。.

Mesalamine has been well used in the improvement of ulcerative colitis (UC) in clinics, however, the underlying mechanisms were not well illustrated. To explore its efficacy from the perspective of gut microbiota and related metabolites, we employed 16S rRNA sequencing and metabolomics approaches in stool samples across 14 normal healthy controls (NC group), 10 treatment-naïve UC patients (UC group) and 14 UC patients responded to mesalamine treatment (mesalamine group). We noted that the gut microbiota diversity and community composition were remarkably perturbed in UC group and partially restored by mesalamine treatment. The relative abundance of 192 taxa in genus level were significantly changed in UC group, and 168 genera were significantly altered after mesalamine intervention. Meanwhile, a total of 127 metabolites were significantly changed in UC group and 129 metabolites were significantly altered after mesalamine treatment. Importantly, we observed that many candidates including 49 genera (such as Escherichia-shigella, Enterococcus and Butyricicoccus) and 102 metatoblites (such as isoleucine, cholic acid and deoxycholic acid) were reversed by mesalamine. Spearman correlation analysis revealed that most of the candidates were significantly correlated with Mayo score of UC, and the relative abundance of specific genera were significant correlated with the perturbation of metabolites. Pathway analysis demonstrated that genera and metabolites candidates were enriched in many similar molecular pathways such as amino acid metabolism and secondary metabolites biosynthesis. Importantly, ROC curve analysis identified a gut microbiota signature composed of five genera including Escherichia-Shigella, Streptococcus, Megamonas, Prevotella_9 and [Eubacterium] _coprostanoligenes _group which might be used to distinguish UC group from both NC and mesalamine group. In all, our results suggested that mesalamine might exert a beneficial role in UC by modulating gut microbiota signature with correlated metabolites in different pathways, which may provide a basis for developing novel candidate biomarkers and therapeutic targets of UC.

Gut microbiota disorders are closely related to polycystic ovarian syndrome (PCOS). Buzhong Yiqi prescription (BZYQ) has a significant clinical effect on the treatment of patients with obesity exhibiting PCOS and phlegm-dampness syndrome caused by spleen deficiency (SPSD). Hence, this study aimed to explore gut microbiota and fecal metabolite alterations in such patients treated with BZYQ. Fifty eligible patients with obesity manifesting PCOS and SPSD participated and agreed to undergo 3 months of BZYQ treatment. Results showed that BZYQ significantly alleviated the serum dehydroepiandrosterone sulfate p < 0.001 and testosterone levels p < 0.001 and markedly changed the gut microbiota structure in these patients. Furthermore, 106 differential fecal metabolites and 14 KEGG enrichment pathways were quantified. The phylum Spirochaetae and the genera [Eubacterium]_rectale_group, Escherichia-Shigella, and Fusicatenibacter were significantly more abundant, but Megamonas was significantly less abundant after treatment than before treatment. Disorders in the gut microbiota and fecal metabolites of these patients were closely related to hyperandrogenemia and insulin resistance. In conclusion, BZYQ could ameliorate the serum androgen level and had an impact on the gut microbiota and metabolites in patients with obesity manifesting PCOS and SPSD.

Trehalose, a nonreducing disaccharide consisting of d-glucose with α,α-1,1 linkage, was evaluated as a functional material to improve the gut environment in preweaned calves. In experiment 1, 173 calves were divided into two groups; the trehalose group was fed trehalose at 30 g/animal/d with milk replacer during the suckling period, and the control group was fed nonsupplemented milk replacer. Medication frequency was lower in the trehalose group (P < 0.05). In experiment 2, calves (n = 20) were divided into two groups (control group [n = 10] and trehalose group [n = 10]) based on their body weight and reared under the same feeding regimens as in experiment 1. Fresh feces were collected from individual animals at the beginning of the trial (average age 11 d), 3 wk after trehalose feeding (experimental day 22), and 1 d before weaning, and the fecal score was recorded daily. Fecal samples were analyzed for fermentation parameters and microbiota. The fecal score was significantly lower in the trehalose group than in the control group in the early stage (at an age of 14 to 18 d; P < 0.05) of the suckling period. Calves fed trehalose tended to have a higher proportion of fecal butyrate on day 22 than calves in the control group (P = 0.08). Population sizes of Clostridium spp. were significantly lower (P = 0.036), whereas those of Dialister spp. and Eubacterium spp. tended to be higher in the feces of calves in the trehalose group on day 22 (P = 0.060 and P = 0.083). These observations indicate that trehalose feeding modulated the gut environment and partially contributed to the reduction in medication frequency observed in experiment 1.

Objective To characterize the cervicovaginal microbiota of HPV-positive and HPV-negative asymptomatic Peruvian women, by identifying the presence of 13 representative bacteria genus. Results A total of 100 HPV-positive and 100 HPV-negative women were matched by age for comparison of microbiota. The following bacteria were more frequently identified in HPV-positive patients compared to HPV-negative: Eubacterium (68 vs 32%), Actinobacteria (46 vs 33%), Fusobacterium (11 vs 6%) and Bacteroides (20 vs 13%). A comparison between high-risk and low-risk genotypes was performed and differences were found in the detection of Actinobacteria (50 vs 33.33%), Bifidobacterium (50 vs 20.83%) and Enterococcus (50 vs 29.17%).

OBJECTIVES: Oral microbiome plays an important role in oral diseases. Among them, proliferative verrucous leucoplakia (PVL) is an uncommon form of progressive multifocal leukoplakia with a worryingly rate of malignant transformation. Here, we aimed to characterize the oral microbiome of PVL patients and compare it with those of healthy controls. MATERIAL AND METHODS: Oral biopsies from ten PVL patients and five healthy individuals were obtained and used to compare their microbial communities. The sequence of the V3-V4 region of 16S rRNA gene was used as the taxonomic basis to estimate and analyze the composition and diversity of bacterial populations present in the samples. RESULTS: Our results show that the oral microbial composition and diversity are significantly different among PVL patients and healthy donors. The average number of observed operational taxonomic units (OTUs) was higher for healthy donors than for PVL, proving a loss of diversity in PVL. Several OTUs were found to be more abundant in either group. Among those that were significantly enriched in PVL patients, potential protumorigenic pathogens like Oribacterium sp. oral taxon 108, Campylobacter jejuni, uncultured Eubacterium sp., Tannerella, and Porphyromonas were identified. CONCLUSION: Oral microbiome dysbiosis was found in patients suffering from PVL. To the best of our knowledge, this is the first study investigating the oral microbiome alterations in PVL and, due to the limited number of participants, additional studies are needed. Oral microbiota-based biomarkers may be helpful in predicting the risks for the development of PVL.

Human milk glycans present a unique diversity of structures that suggest different mechanisms by which they may affect the infant microbiome development. A humanized mouse model generated by infant fecal transplantation was utilized here to evaluate the impact of fucosyl-α1,3-GlcNAc (3FN), fucosyl-α1,6-GlcNAc, lacto-N-biose (LNB) and galacto-N-biose on the fecal microbiota and host–microbiota interactions. 16S rRNA amplicon sequencing showed that certain bacterial genera significantly increased (Ruminococcus and Oscillospira) or decreased (Eubacterium and Clostridium) in all disaccharide-supplemented groups. Interestingly, cluster analysis differentiates the consumption of fucosyl-oligosaccharides from galactosyl-oligosaccharides, highlighting the disappearance of Akkermansia genus in both fucosyl-oligosaccharides. An increment of the relative abundance of Coprococcus genus was only observed with 3FN. As well, LNB significantly increased the relative abundance of Bifidobacterium, whereas the absolute levels of this genus, as measured by quantitative real-time PCR, did not significantly increase. OTUs corresponding to the species Bifidobacterium longum, Bifidobacterium adolescentis and Ruminococcus gnavus were not present in the control after the 3-week intervention, but were shared among the donor and specific disaccharide groups, indicating that their survival is dependent on disaccharide supplementation. The 3FN-feeding group showed increased levels of butyrate and acetate in the colon, and decreased levels of serum HDL-cholesterol. 3FN also down-regulated the pro-inflammatory cytokine TNF-α and up-regulated the anti-inflammatory cytokines IL-10 and IL-13, and the Toll-like receptor 2 in the large intestine tissue. The present study revealed that the four disaccharides show efficacy in producing beneficial compositional shifts of the gut microbiota and in addition, the 3FN demonstrated physiological and immunomodulatory roles., This work was supported by the Spanish Ministry for Economy and Competitiveness (MINECO)/FEDER under Grant AGL2017-84165-C2 (1-R and 2-R). JRD was supported by a Ramon y Cajal Contract RYC-2013-12442 by the Spanish Ministry for Economy and Competitiveness and by Valencian Government/FEDER grant IDIFEDER/2018/056. EMMG was supported by a pre-doctoral Contract PRE2018-085768 by the Spanish Ministry of Science, Innovation and Universities.

Gut microbiota appears to be involved in the pathogenesis of primary sclerosing cholangitis (PSC). The protein tyrosine phosphatase nonreceptor 2 (PTPN2) gene risk variant rs1893217 is associated with gut dysbiosis in inflammatory bowel disease (IBD), and PTPN2 was mentioned as a possible risk gene for PSC. This study assessed the microbial profile of ulcerative colitis (UC) patients with PSC and without PSC (non-PSC). Additionally, effects of the PTPN2 risk variant were assessed. In total, 216 mucosal samples from ileum, colon, and rectum were collected from 7 PSC and 42 non-PSC patients, as well as 28 control subjects (non-IBD). The microbial composition was derived from 16S rRNA sequencing data. Overall, bacterial richness was highest in PSC patients, who also had a higher relative abundance of the genus Roseburia compared to non-PSC, as well as Haemophilus, Fusobacterium, Bifidobacterium, and Actinobacillus compared to non-IBD, as well as a lower relative abundance of Bacteroides compared to non-PSC and non-IBD, respectively. After exclusion of patients with the PTPN2 risk variant, Brachyspira was higher in PSC compared to non-PSC, while, solely in colon samples, Eubacterium and Tepidimonas were higher in PSC vs. non-IBD. In conclusion, this study underlines the presence of gut mucosa-associated microbiome changes in PSC patients and rather weakens the role of PTPN2 as a PSC risk gene.

Most cirrhosis etiologies, such as alcohol, hepatitis C, and obesity, involve behavior that require the loss of inhibitory control. Once cirrhosis develops, patients can also develop cognitive impairment due to minimal hepatic encephalopathy (MHE). Both processes could have distinct imprints on the gut-liver-brain axis. Determine the impact of inhibitory control versus traditional cirrhosis-related cognitive performance on gut microbial composition and function. Outpatients with cirrhosis underwent two tests for MHE: inhibitory control test (MHEICT, computerized associated with response inhibition) and psychometric hepatic encephalopathy score (MHEPHES, paper-pencil HE-specific associated with subcortical impairment) along with stool collection for metagenomics. MHEICT/not, MHEPHES/not, and discordant (positive on one test but negative on the other) were analyzed for demographics, bacterial species, and gut-brain modules (GBM) using multi-variable analyses. Ninety-seven patients [47 (49%) MHEPHES, 76 (78%) MHEICT, 41 discordant] were enrolled. MHEPHES/not: Cirrhosis severity was worse in MHEPHES without differences in alpha/beta diversity on bacterial species or GBMs. Pathobionts (Enterobacteriaceae) and γ-amino-butryic acid (GABA) synthesis GBM were higher in MHEPHES. MHEICT/not: We found similar cirrhosis severity and metagenomic alpha/beta diversity in MHEICT versus not. However, alpha/beta diversity of GBMs were different in MHEICT versus No-MHE patients. Alistipes ihumii, Prevotella copri, and Eubacterium spp. were higher, while Enterococcus spp. were uniquely lower in MHEICT versus no-MHE and discordant comparisons. GBMs belonging to tryptophan, menaquinone, GABA, glutamate, and short-chain fatty acid synthesis were also unique to MHEICT. Gut microbial signature of impaired inhibitory control, which is associated with addictive disorders that can lead to cirrhosis, is distinct from cirrhosis-related cognitive impairment.

Mastitis is one of the major problems for the productivity of dairy cows and its classifications have usually been based on milk somatic cell counts (SCCs). In this study, we investigated the differences in milk production, rumen fermentation parameters, and diversity and composition of rumen and hindgut bacteria in cows with similar SCCs with the aim to identify whether they can be potential microbial biomarkers to improve the diagnostics of mastitis. A total of 20 dairy cows with SCCs over 500 &times, 103 cells/mL in milk but without clinical symptoms of mastitis were selected in this study. Random forest modeling revealed that Erysipelotrichaceae UCG 004 and the [Eubacterium] xylanophilum group in the rumen, as well as the Family XIII AD3011 group and Bacteroides in the hindgut, were the most influential candidates as key bacterial markers for differentiating &ldquo, true&rdquo, mastitis from cows with high SCCs. Mastitis statuses of 334 dairy cows were evaluated, and 96 in 101 cows with high SCCs were defined as healthy rather than mastitis according to the rumen bacteria. Our findings suggested that bacteria in the rumen and hindgut can be a new approach and provide an opportunity to reduce common errors in the detection of mastitis.

ObjectiveMultiple clinical similarities exist between IgG4-related sclerosing cholangitis (IgG4-SC) and primary sclerosing cholangitis (PSC), and while gut dysbiosis has been extensively studied in PSC, the role of the gut microbiota in IgG4-SC remains unknown. Herein, we aimed to evaluate alterations of the gut microbiome and metabolome in IgG4-SC and PSC.DesignWe performed 16S rRNA gene amplicon sequencing of faecal samples from 135 subjects with IgG4-SC (n=34), PSC (n=37) and healthy controls (n=64). A subset of the samples (31 IgG4-SC, 37 PSC and 45 controls) also underwent untargeted metabolomic profiling.ResultsCompared with controls, reduced alpha-diversity and shifted microbial community were observed in IgG4-SC and PSC. These changes were accompanied by differences in stool metabolomes. Importantly, despite some common variations in the microbiota composition and metabolic activity, integrative analyses identified distinct host–microbe associations in IgG4-SC and PSC. The disease-associated genera and metabolites tended to associate with the transaminases in IgG4-SC. Notable depletion ofBlautiaand elevated succinic acid may underlie hepatic inflammation in IgG4-SC. In comparison, potential links between the microbial or metabolic signatures and cholestatic parameters were detected in PSC. Particularly, concordant decrease ofEubacteriumand microbiota-derived metabolites, including secondary bile acids, implicated novel host–microbial metabolic pathways involving cholestasis of PSC. Interestingly, the predictive models based on metabolites were more effective in discriminating disease status than those based on microbes.ConclusionsOur data reveal that IgG4-SC and PSC possess divergent host–microbe interplays that may be involved in disease pathogenesis. These data emphasise the uniqueness of IgG4-SC.