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Microbiology Spectrum Aug 2023Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the...
Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of the gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (controls [CTRL]). The top three relatively abundant microbes in both groups were Escherichia coli, , and , followed by and . E. coli, , and were found to be increased in the CTRL group, whereas and were greater in the ABF group. The highest abundances of antibiotic resistance proteins (log expression levels [ELs] of >10) were found to be for tetracycline resistance (Tet) and aminoglycoside resistance (AMG) proteins found in , with a significant increase in the CTRL group. High Tet (ELs of 5.32) was found in in the CTRL group, although pigs in both groups had never received tetracycline, possibly reflecting the influence of environments in farms. In E. coli, AMG and β-lactamase family proteins were observed in both groups (ELs of 3 to 6), whereas multidrug resistance protein MdtL was significantly expressed in the CTRL group (ELs of around 3). In the ABF group, CRISPR-associated endonucleases Cas1 and Cas9, which function to defend against viruses, were markedly observed in and , respectively, with ELs of 8.6 and 4.15, respectively. In conclusion, this study demonstrated that CRISPR-associated endonucleases were markedly observed in the ABF group, whereas higher levels of Tet, AMG, and multidrug resistance protein MdtL was markedly observed in dominant bacterial species in the CTRL group. In order to control and reduce antibiotic use in animals, the Department of Livestock Development, Thailand, has launched a campaign for antibiotic-free livestock production. The present study has shown for the first time that CRISPR-associated endonucleases Cas1 and Cas9, which function to defend against viruses, were markedly observed in and , respectively, in ceca of pigs raised without antibiotics (ABF). The highest abundances of antibiotic resistance proteins were for tetracycline (Tet) and aminoglycoside resistance (AMG) proteins found in , with a significant increase in the controls. In E. coli, the microbe with the highest relative abundance, AMG and β-lactamase family proteins were observed in both groups, whereas multidrug resistance protein MdtL was significantly expressed in the controls. Pigs in both ABF and control groups had never received tetracycline, possibly reflecting the influence of farm environments. We suggest that pigs raised without antibiotics may have more beneficial microorganisms for the gut than pigs raised with antibiotics.
Topics: Swine; Animals; Anti-Bacterial Agents; Escherichia coli; Microbiota; Tetracycline; Bacteria; beta-Lactamases; Aminoglycosides; ATP Binding Cassette Transporter, Subfamily B
PubMed: 37439677
DOI: 10.1128/spectrum.02223-23 -
Neoplasia (New York, N.Y.) Sep 2023We have previously demonstrated abnormal gut microbial composition in castration-resistant prostate cancer (CRPC) patients, here we revealed the mechanism of gut...
We have previously demonstrated abnormal gut microbial composition in castration-resistant prostate cancer (CRPC) patients, here we revealed the mechanism of gut microbiota-derived short-chain fatty acids (SCFAs) as a mediator linking CRPC microbiota dysbiosis and prostate cancer (PCa) progression. By using transgenic TRAMP mouse model, PCa patient samples, in vitro PCa cell transwell and macrophage recruitment assays, we examined the effects of CRPC fecal microbiota transplantation (FMT) and SCFAs on PCa progression. Our results showed that FMT with CRPC patients' fecal suspension increased SCFAs-producing gut microbiotas such as Ruminococcus, Alistipes, Phascolarctobaterium in TRAMP mice, and correspondingly raised their gut SCFAs (acetate and butyrate) levels. CRPC FMT or SCFAs supplementation significantly accelerated mice's PCa progression. In vitro, SCFAs enhanced PCa cells migration and invasion by inducing TLR3-triggered autophagy that further activated NF-κB and MAPK signalings. Meanwhile, autophagy of PCa cells released higher level of chemokine CCL20 that could reprogramme the tumor microenvironment by recruiting more macrophage infiltration and simultaneously polarizing them into M2 type, which in turn further strengthened PCa cells invasiveness. Finally in a cohort of 362 PCa patients, we demonstrated that CCL20 expression in prostate tissue was positively correlated with Gleason grade, pre-operative PSA, neural/seminal vesical invasion, and was negatively correlated with post-operative biochemical recurrence-free survival. Collectively, CRPC gut microbiota-derived SCFAs promoted PCa progression via inducing cancer cell autophagy and M2 macrophage polarization. CCL20 could become a biomarker for prediction of prognosis in PCa patients. Intervention of SCFAs-producing microbiotas may be a useful strategy in manipulation of CRPC.
Topics: Gastrointestinal Microbiome; Fatty Acids, Volatile; Disease Progression; Autophagy; Macrophages; Cell Polarity; Ruminococcus; Prostatic Neoplasms, Castration-Resistant; Mice, Transgenic; Bacteroidetes; Veillonellaceae; Fecal Microbiota Transplantation; Humans; Male; Animals; Mice
PubMed: 37579688
DOI: 10.1016/j.neo.2023.100928 -
Scientific Reports Apr 2022Mycoplasma pneumoniae (MP) infection is a common cause of community-acquired pneumonia in children. Furthermore, many children with Mycoplasma pneumoniae pneumonia (MPP)...
Mycoplasma pneumoniae (MP) infection is a common cause of community-acquired pneumonia in children. Furthermore, many children with Mycoplasma pneumoniae pneumonia (MPP) have recurrent wheezing and reduced small airway function after their clinical symptoms have resolved, eventually leading to asthma. MPP can trigger immune disorders and systemic inflammatory responses. Hence, the intestine is the largest immune organ of the body. Therefore, we sought to investigate whether the alteration of intestinal flora is correlated with the development of wheezing in children with MPP. We collected 30 healthy children as group A, 50 children with nonwheezing MPP as group B, and 50 children with wheezing MPP as group C. We found that the percentage of eosinophil cells (EC) was significantly higher in group C than that in group B for routine blood tests and serum inflammatory factors. The serum cytokines, including IL-4, IL-17, TNF-α, and TGF-β, were significantly higher in group C than in group B. In addition, the level of IL-10 was significantly lower in group C than in group B. The distribution characteristics of intestinal flora strains in children with MPP were detected by sequencing of 16S rRNA gene amplicon sequencing. There were differences in the abundance of intestinal flora between children with MPP and healthy children, with lower abundance of Ruminococcus flavefaciens, Clostridium butyricum, Lactobacillus, and Bifidobacterium in the intestine of children with MPP compared to healthy children. The abundance of Ruminococcus flavefaciens and Clostridium butyricum was significantly lower in the intestine of children with wheezing MPP compared to children without wheezing MPP. In the correlation analysis between children with MPP and inflammatory factors, Ruminococcus flavefaciens was found to be negatively correlated with IL-17. Clostridium butyricum was negatively correlated with L-4, IL-17, TNF-α, and TGF-β; however, it positively correlated with IL-10. Thus, it was concluded that alterations in intestinal flora play a crucial role in the immune response to MPP, where a significant decline in intestinal Ruminococcus flavefaciens and Clostridium butyricum leads to an exacerbation of the inflammatory responses, which may promote the development of children with wheezing MPP.
Topics: Child; Gastrointestinal Microbiome; Humans; Mycoplasma pneumoniae; Pneumonia, Mycoplasma; RNA, Ribosomal, 16S; Respiratory Sounds
PubMed: 35383237
DOI: 10.1038/s41598-022-09700-0 -
Journal, Genetic Engineering &... Apr 2021Cellulose is the primary component of the plant cell wall and an important source of energy for the ruminant and microbial protein synthesis in the rumen. Cell wall...
BACKGROUND
Cellulose is the primary component of the plant cell wall and an important source of energy for the ruminant and microbial protein synthesis in the rumen. Cell wall content is digested by anaerobic fermentation activity mainly of bacteria belonging to species Fibrobacter succinogenes, Ruminicoccus albus, Ruminococcus flavefaciens, and Butyrivibrio fibrisolvens. Bacteria belonging to the species Ruminococcus albus contain cellulosomes that enable it to adhere to and digest cellulose, and its genome encodes cellulases and hemicellulases. This study aimed to perform an in silico comparative characterization and functional analysis of cellulase from Ruminococcus albus to explore physicochemical properties and to estimate primary, secondary, and tertiary structure using various bio-computational tools. The protein sequences of cellulases belonging to 6 different Ruminococcus albus strains were retrieved using UniProt. In in silico composition of amino acids, basic physicochemical characteristics were analyzed using ProtParam and Protscale. Multiple sequence alignment of retrieved sequences was performed using Clustal Omega and the phylogenetic tree was constructed using Mega X software. Bioinformatics tools are used to better understand and determine the 3D structure of cellulase. The predicted model was refined by ModRefiner. Structure alignment between the best-predicted model and the template is applied to evaluate the similarity between structures.
RESULTS
In this study are demonstrated several physicochemical characteristics of the cellulase enzyme. The instability index values indicate that the proteins are highly stable. Proteins are dominated by random coils and alpha helixes. The aliphatic index was higher than 71 providing information that the proteins are highly thermostable. No transmembrane domain was found in the protein, and the enzyme is extracellular and moderately acidic. The best tertiary structure model of the enzyme was obtained by the use of Raptor X, which was refined by ModRefiner. Raptor X suggested the 6Q1I_A as one of the best homologous templates for the predicted 3D protein structure. Ramachandran plot analysis showed that 90.1% of amino acid residues are within the most favored regions.
CONCLUSIONS
This study provides for the first time insights about the physicochemical properties, structure, and function of cellulase, from Ruminococcus albus, that will help for detection and identification of such enzyme in vivo or in silico.
PubMed: 33871739
DOI: 10.1186/s43141-021-00162-x -
Nephrology, Dialysis, Transplantation :... Aug 2021The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response...
BACKGROUND
The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response regulation, has gained interest in the development of CKD therapies. However, reports using shotgun metagenomic analysis of the gut microbiome are scarce, especially for early CKD. Here we characterized gut microbiome differences between non-CKD participants and ones with early CKD using metagenomic sequencing.
METHODS
In total, 74 non-CKD participants and 37 participants with early CKD were included based on propensity score matching, controlling for various factors including dietary intake. Stool samples were collected from participants and subjected to shotgun sequencing. Bacterial and pathway abundances were profiled at the species level with MetaPhlAn2 and HUMAnN2, respectively, and overall microbiome differences were determined using Bray-Curtis dissimilarities. Diabetic and non-diabetic populations were analysed separately.
RESULTS
For diabetic and non-diabetic participants, the mean estimated glomerular filtration rates of the CKD group were 53.71 [standard deviation (SD) 3.87] and 53.72 (SD 4.44), whereas those of the non-CKD group were 72.63 (SD 7.72) and 76.10 (SD 9.84), respectively. Alpha and beta diversities were not significantly different between groups. Based on taxonomic analysis, butyrate-producing species Roseburia inulinivorans, Ruminococcus torques and Ruminococcus lactaris were more abundant in the non-CKD group, whereas Bacteroides caccae and Bacteroides coprocora were more abundant in the non-diabetic CKD group.
CONCLUSIONS
Although gut microbiome changes in individuals with early CKD were subtle, the results suggest that changes related to producing short-chain fatty acids can already be observed in early CKD.
Topics: Bacteroides; Clostridiales; Gastrointestinal Microbiome; Humans; Renal Insufficiency, Chronic; Ruminococcus
PubMed: 32869063
DOI: 10.1093/ndt/gfaa122 -
JHEP Reports : Innovation in Hepatology Jan 2023Sarcopenia and gut dysbiosis are common in individuals with cirrhosis. However, the association between sarcopenia and microbial alterations, and the subsequent impact...
BACKGROUND & AIMS
Sarcopenia and gut dysbiosis are common in individuals with cirrhosis. However, the association between sarcopenia and microbial alterations, and the subsequent impact on cirrhotic outcomes are poorly understood. This study aimed to identify muscle-dependent microbial changes and related risks of cirrhotic complications.
METHODS
From September 2018 to December 2020, 89 individuals with cirrhosis and 16 healthy volunteers were prospectively enrolled. Muscle and nutritional status, serum amino acids, and fecal microbiota were analyzed. The association between microbial signatures of sarcopenia and cirrhotic complications was investigated.
RESULTS
A decline in muscle mass and strength were associated with gut microbial alterations in individuals with cirrhosis. The greatest microbial dissimilarity was observed between those with sarcopenia (both decline in muscle mass and strength) and those with normal-muscle status ( = 0.035). Individuals with sarcopenia had lower serum levels of alanine, valine, leucine, isoleucine, proline, tryptophan and ornithine. Besides, gut microbial functions associated with amino acid biosynthesis were significantly reduced in individuals with sarcopenia and cirrhosis. Depletion of , and were associated with cirrhotic sarcopenia, and significantly correlated with the serum levels of amino acids. Individuals with coexistent depletion of and developed more infectious (44.4% . 3.0%) and non-infectious (74.1% 3.0%) complications, and more hospitalizations (54 3) than those with cirrhosis with good microbial signatures (all <0.001). In contrast, fecal enrichment of and independently decreased the risk of 1-year complications.
CONCLUSIONS
Sarcopenia-related fecal microbial alterations are associated with cirrhotic complications. These findings may facilitate measures to improve the outcomes of individuals with cirrhosis and sarcopenia by modifying gut microbiota.
IMPACT AND IMPLICATIONS
The composition and biosynthetic functions of gut microbiota are significantly changed in individuals with sarcopenic cirrhosis. Those with a sarcopenia-related poor microbial signature, in which and were both depleted, had significantly more infectious and non-infectious complications, as well as more hospitalizations. These findings highlight the therapeutic potential of modifying the gut microbiota of individuals with sarcopenic cirrhosis to improve their clinical outcomes.
PubMed: 36536957
DOI: 10.1016/j.jhepr.2022.100619 -
BioMed Research International 2021The subjects included 13 PI patients from the Hubei Provincial Hospital of TCM, Hubei University of TCM, and Wuhan Traditional Chinese Medicine Hospital, and the... (Clinical Trial)
Clinical Trial
METHODS
The subjects included 13 PI patients from the Hubei Provincial Hospital of TCM, Hubei University of TCM, and Wuhan Traditional Chinese Medicine Hospital, and the corresponding noninsomniac spouses of the patients were selected as controls. TWBXG was continuously administered for 4 weeks. The feces of PI patients and their noninsomniac spouses before and after treatment with TWBXG were collected. The intestinal flora composition of each group was detected by metagenomic sequencing, and the efficacy of TWBXG was evaluated by the PSQI scale.
RESULTS
Compared with the control group, the model group showed an increase in the abundance of Roseburia faecis, Ruminococcus, Prevotella copri, Fusicatenibacter saccharivorans, and Blautia obeum, while those of Bacteroides, fecal Bacteroidetes, and Faecalibacterium prausnitzii were decreased. Compared with pretreatment, the PSQI score was significantly reduced ( < 0.05), the abundance of Bacteroides, fecal Bacteroidetes, and Faecalibacterium prausnitzii increased, and that of Roseburia faecis, Ruminococcus, Prevotella copri, Fusicatenibacter saccharivorans, and Blautia obeum decreased after treatment. However, there was still a certain gap in the abundance of related flora in the treatment group compared with the control.
CONCLUSION
PI is associated with disturbances in the intestinal flora and is mainly related to the disorders of Roseburia faecis, Ruminococcus, Prevotella copri, Fusicatenibacter saccharivorans, Blautia obeum, Bacteroides, fecal Bacteroidetes, and Faecalibacterium prausnitzii. TWBXG can effectively treat PI, and its effect may be achieved by regulating the disordered intestinal flora. The study was registered in the Chinese clinical trial registry and approved by the World Health Organization clinical trial registration platform (Effects of the modified Tianwang Buxin granule and modified Tianwang Buxin decoction pieces on insomnia: a randomized, controlled trial, ChiCTR-IPR-17011549).
Topics: Adult; Case-Control Studies; Drugs, Chinese Herbal; Female; Gastrointestinal Microbiome; Hot Flashes; Humans; Male; Middle Aged; Perimenopause; Phytotherapy; Sleep Initiation and Maintenance Disorders
PubMed: 34825005
DOI: 10.1155/2021/9979511 -
Journal of Endocrinological... Sep 2021The imbalance of gut microbiota has been linked to manifold endocrine diseases, but the association with Graves' disease (GD) is still unclear. The purpose of this study...
OBJECTIVE
The imbalance of gut microbiota has been linked to manifold endocrine diseases, but the association with Graves' disease (GD) is still unclear. The purpose of this study was to investigate the correlation between human gut microbiota and clinical characteristics and thyroidal functional status of GD.
METHODS
14 healthy volunteers (CG) and 15 patients with primary GD (HG) were recruited as subjects. 16SrDNA high-throughput sequencing was performed on IlluminaMiSeq platform to analyze the characteristics of gut microbiota in patients with GD. Among them, the thyroid function of 13 patients basically recovered after treatment with anti-thyroid drugs (oral administration of Methimazole for 3-5 months). The fecal samples of patients after treatment (TG) were sequenced again, to further explore and investigate the potential relationship between dysbacteriosis and GD.
RESULTS
In terms of alpha diversity index, the observed OTUs, Simpson and Shannon indices of gut microbiota in patients with GD were significantly lower than those in healthy volunteers (P < 0.05).The difference of bacteria species was mainly reflected in the genus level, in which the relative abundance of Lactobacillus, Veillonella and Streptococcus increased significantly in GD. After the improvement of thyroid function, a significant reduction at the genus level were Blautia, Corynebacter, Ruminococcus and Streptococcus, while Phascolarctobacterium increased significantly (P < 0.05). According to Spearman correlation analysis, the correlation between the level of thyrotropin receptor antibody (TRAb) and the relative abundance of Lactobacillus and Ruminococcus was positive, while Synergistetes and Phascolarctobacterium showed a negative correlation with TRAb. Besides, there were highly significant negative correlation between Synergistetes and clinical variables of TRAb, TPOAb and TGAb (P < 0.05, R < - 0.6).
CONCLUSIONS
This study revealed that functional status and TRAb level in GD were associated with composition and biological function in the gut microbiota, with Synergistetes and Phascolarctobacterium protecting the thyroid probably, while Ruminococcus and Lactobacillus may be novel biomarkers of GD.
Topics: Adult; Antithyroid Agents; Asian People; Feces; Female; Gastrointestinal Microbiome; Graves Disease; Healthy Volunteers; High-Throughput Nucleotide Sequencing; Humans; Lactobacillus; Male; Methimazole; Receptors, Thyrotropin; Ruminococcus; Thyroid Function Tests; Young Adult
PubMed: 33481211
DOI: 10.1007/s40618-021-01507-6 -
Experimental Dermatology Dec 2021Symptomatic dermographism (SD) is a recurrent inflammatory skin disease related to immunity; however, the details remain elusive. In view of the important role of gut...
Symptomatic dermographism (SD) is a recurrent inflammatory skin disease related to immunity; however, the details remain elusive. In view of the important role of gut microbiota in immune regulation, the purpose of this study is to investigate the alterations of gut microbiota in SD and explore the potential bacterial biomarkers for diagnosis. A case-control study including SD patients and normal controls (NCs) was carried out. Gut microbiota of the participants was analysed by the 16S rDNA sequencing of faecal samples. The linear discriminant analysis effect size and the receiver operating characteristic curve (ROC) analysis were used to identify the bacterial biomarkers. Forty-four participants were included in this study. The alpha-diversity and beta-diversity of gut microbiota differed significantly between SD patients and NCs. The abundance of Verrucomicrobia, Ruminococcaceae and their subordinate taxa were reduced in SD patients, while Enterobacteriales and its subordinate taxon exhibited higher relative abundance compared with NCs. Subdoligranulum and Ruminococcus bromii showed a potential diagnostic value for SD, and Prevotella stercorea was negatively relevant to duration of SD. Furthermore, the pyruvate, butyric acid and histamine metabolism pathway were likely to be involved in the pathogenesis of SD. Our results revealed that the gut microbiota of SD patients experienced obvious changes, and Verrucomicrobia, Ruminococcaceae and Enterobacteriales were microbiota signatures for SD.
Topics: Adult; Biomarkers; Case-Control Studies; Feces; Female; Gastrointestinal Microbiome; Humans; Male; ROC Curve; Ruminococcus; Sensitivity and Specificity; Urticaria
PubMed: 33751677
DOI: 10.1111/exd.14326 -
Scientific Reports Nov 2022Moyamoya disease (MMD) is a rare cerebrovascular disease endemic in East Asia. The p.R4810K mutation in RNF213 gene confers a risk of MMD, but other factors remain...
Moyamoya disease (MMD) is a rare cerebrovascular disease endemic in East Asia. The p.R4810K mutation in RNF213 gene confers a risk of MMD, but other factors remain largely unknown. We tested the association of gut microbiota with MMD. Fecal samples were collected from 27 patients with MMD, 7 patients with non-moyamoya intracranial large artery disease (ICAD) and 15 control individuals with other disorders, and 16S rRNA were sequenced. Although there was no difference in alpha diversity or beta diversity between patients with MMD and controls, the cladogram showed Streptococcaceae was enriched in patient samples. The relative abundance analysis demonstrated that 23 species were differentially abundant between patients with MMD and controls. Among them, increased abundance of Ruminococcus gnavus > 0.003 and decreased abundance of Roseburia inulinivorans < 0.002 were associated with higher risks of MMD (odds ratio 9.6, P = 0.0024; odds ratio 11.1, P = 0.0051). Also, Ruminococcus gnavus was more abundant and Roseburia inulinivorans was less abundant in patients with ICAD than controls (P = 0.046, P = 0.012). The relative abundance of Ruminococcus gnavus or Roseburia inulinivorans was not different between the p.R4810K mutant and wildtype. Our data demonstrated that gut microbiota was associated with both MMD and ICAD.
Topics: Humans; Moyamoya Disease; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Ruminococcus; Intracranial Arterial Diseases; Rare Diseases; Arteries; Adenosine Triphosphatases; Ubiquitin-Protein Ligases
PubMed: 36424438
DOI: 10.1038/s41598-022-24496-9