-
World Journal of Gastroenterology Apr 2012To characterize the colon microbiota in two women histologically diagnosed with collagenous colitis using a culture-independent method.
AIM
To characterize the colon microbiota in two women histologically diagnosed with collagenous colitis using a culture-independent method.
METHODS
Biopsies were taken from the ascending colon and the total DNA was extracted. Universal bacterial primers were used to amplify the bacterial 16S rRNA genes. The amplicons were then cloned into competent Escherichia coli cells. The clones were sequenced and identified by comparison to known sequences.
RESULTS
The clones could be divided into 44 different phylotypes. The microbiota was dominated by Firmicutes and Bacteroidetes. Seven phylotypes were found in both patients and constituted 47.5% of the total number of clones. Of these, the most dominating were clones similar to Bacteroides cellulosilyticus, Bacteroides caccae, Bacteroides thetaiotaomicron, Bacteroides uniformis and Bacteroides dorei within Bacteroidetes. Sequences similar to Faecalibacterium prausnitzii and Clostridium citroniae were also found in both patients.
CONCLUSION
A predominance of potentially pathogenic Bacteroides spp., and the presence of clones showing similarity to Clostridium clostridioforme were found but the overall colon microbiota showed similarities to a healthy one. Etiologies for collagenous colitis other than an adverse bacterial flora must also be considered.
Topics: Bacteria; Bacteroides; Clostridium; Colitis, Collagenous; Colon; DNA Primers; DNA, Bacterial; Female; Genes, rRNA; Humans; Metagenome; Middle Aged; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 22529692
DOI: 10.3748/wjg.v18.i14.1628 -
BMC Research Notes Feb 2021Differential alterations in gut microbiota and chronic low-grade inflammation play a critical role in the development of Type 2 diabetes (T2D). Here we aimed to...
OBJECTIVE
Differential alterations in gut microbiota and chronic low-grade inflammation play a critical role in the development of Type 2 diabetes (T2D). Here we aimed to investigate if dysbiosis of inflammation and anti-inflammation-associated gut bacterial communities in fecal samples of individuals had any influence on T2D using a 16S rRNA gene of V3 region sequencing at Illumina MiSeq platform.
RESULTS
Our findings showed that a higher abundance of inflammatory bacteria such as Lactobacillus ruminis, Ruminococcus gnavus, Bacteroides caccae, Butyricimonas, and Collinsella aerofaciens, and lower abundance of anti-inflammatory bacteria such as Faecalibacterium prausnitzii, and Butyrivibrio that likely play a role in the development of T2D. Our findings hint the potential of indigenous microbiota in developing diagnostic markers and therapeutic targets in T2D.
Topics: Actinobacteria; Anti-Inflammatory Agents; Bacteria; Bacteroides; Clostridiales; Diabetes Mellitus, Type 2; Dysbiosis; Feces; Gastrointestinal Microbiome; Humans; Lactobacillus; Pilot Projects; RNA, Ribosomal, 16S
PubMed: 33549142
DOI: 10.1186/s13104-021-05466-2 -
Nutrients Aug 2023Different research studies have identified specific groups or certain dietary compounds as the onset and progression of obesity and suggested that gut microbiota is a...
Different research studies have identified specific groups or certain dietary compounds as the onset and progression of obesity and suggested that gut microbiota is a mediator between these compounds and the inflammation associated with pathology. In this study, the objective was to evaluate the dietary intake of 108 overweight (OW), obese (OB), and normal-weight (NW) individuals and to analyze their gut microbiota profile to determine changes and associations with Body Mass Index (BMI) and diet. When individuals were compared by BMI, significant differences in fiber and monounsaturated fatty acids (MUFAs) intake were observed, showing higher adequacy for the NW group. The analysis of gut microbiota showed statistical differences for 18 ASVs; and decreased in the OW/OB group, whereas the genus increased; the genus was also found in the LEFSe analysis as a biomarker for OW/OB. was found in a significantly higher proportion of NW individuals and identified as a biomarker for the NW group. Correlation analysis showed that adequation to nutritional recommendation for fiber indicated a higher abundance of , linearly correlated with , , and . The same correlation was found for the adequation for MUFAs, with these bacteria being more abundant when the intake was adjusted to or below the recommendations.
Topics: Humans; Overweight; Gastrointestinal Microbiome; Obesity; Diet; Body Mass Index; Biomarkers
PubMed: 37571355
DOI: 10.3390/nu15153418 -
Antimicrobial Agents and Chemotherapy Sep 1999Gemifloxacin mesylate (SB 265805), a new fluoronaphthyridone, was tested against 359 recent clinical anaerobic isolates by the National Committee for Clinical Laboratory... (Comparative Study)
Comparative Study
Gemifloxacin mesylate (SB 265805), a new fluoronaphthyridone, was tested against 359 recent clinical anaerobic isolates by the National Committee for Clinical Laboratory Standards reference agar dilution method with supplemented brucella blood agar and an inoculum of 10(5) CFU/spot. Comparative antimicrobials tested included trovafloxacin, levofloxacin, grepafloxacin, sparfloxacin, sitafloxacin (DU-6859a), penicillin G, amoxicillin clavulanate, imipenem, cefoxitin, clindamycin, and metronidazole. The MIC(50) and MIC(90) (MICs at which 50 and 90% of the isolates were inhibited) of gemifloxacin against various organisms (with the number of strains tested in parentheses) were as follows (in micrograms per milliliter): for Bacteroides fragilis (28), 0.5 and 2; for Bacteroides thetaiotaomicron (24), 1 and 16; for Bacteroides caccae (12), 1 and 16; for Bacteroides distasonis (12), 8 and >16; for Bacteroides ovatus (12), 4 and >16; for Bacteroides stercoris (12), 0.5 and 0.5; for Bacteroides uniformis (12), 1 and 4; for Bacteroides vulgatus (11), 4 and 4; for Clostridium clostridioforme (15), 0.5 and 0.5; for Clostridium difficile (15), 1 and >16; for Clostridium innocuum (13), 0.125 and 2; for Clostridium perfringens (13), 0.06 and 0.06; for Clostridium ramosum (14), 0.25 and 8; for Fusobacterium nucleatum (12), 0.125 and 0.25; for Fusobacterium necrophorum (11), 0.25 and 0.5; for Fusobacterium varium (13), 0.5 and 1; for Fusobacterium spp. (12), 1 and 2; for Peptostreptococcus anaerobius (13), 0.06 and 0.06; for Peptostreptococcus asaccharolyticus (13), 0.125 and 0.125; for Peptostreptococcus magnus (14), 0.03 and 0.03; for Peptostreptococcus micros (12), 0.06 and 0.06; for Peptostreptococcus prevotii (14), 0.06 and 0.25; for Porphyromonas asaccharolytica (11), 0.125 and 0.125; for Prevotella bivia (10), 8 and 16; for Prevotella buccae (10), 2 and 2; for Prevotella intermedia (10), 0.5 and 0.5; and for Prevotella melaninogenica (11), 1 and 1. Gemifloxacin mesylate (SB 265805) was 1 to 4 dilutions more active than trovafloxacin against fusobacteria and peptostreptococci, and the two drugs were equivalent against clostridia and P. asaccharolytica. Gemifloxacin was equivalent to sitafloxacin (DU 6859a) against peptostreptococci, C. perfringens, and C. ramosum, and sitafloxacin was 2 to 3 dilutions more active against fusobacteria. Sparfloxacin, grepafloxacin, and levofloxacin were generally less active than gemifloxacin against all anaerobes.
Topics: Anti-Bacterial Agents; Anti-Infective Agents; Bacteria, Anaerobic; Fluoroquinolones; Gemifloxacin; Microbial Sensitivity Tests; Naphthyridines; Therapeutic Equivalency
PubMed: 10471570
DOI: 10.1128/AAC.43.9.2231 -
Therapeutic Advances in Medical Oncology 2019There are close links between chemotherapy-induced intestinal mucositis and microbiota dysbiosis. Previous studies indicated that D-methionine was an excellent candidate...
BACKGROUND
There are close links between chemotherapy-induced intestinal mucositis and microbiota dysbiosis. Previous studies indicated that D-methionine was an excellent candidate for a chemopreventive agent. Here, we investigated the effects of D-methionine on cisplatin-induced mucositis.
MATERIALS AND METHODS
Male Wistar rats (176-200 g, 6 weeks old) were given cisplatin (5 mg/kg) and treated with D-methionine (300 mg/kg). Histopathological, digestive enzymes activity, oxidative/antioxidant status, proinflammatory/anti-inflammatory cytokines in intestinal tissues were measured. Next-generation sequencing technologies were also performed to investigate the gut microbial ecology.
RESULTS
D-methionine administration increased villus length and crypt depth and improved digestive enzyme (leucine aminopeptidase, sucrose and alkaline phosphatase) activities in the brush-border membrane of cisplatin-treated rats ( < 0.05). Furthermore, D-methionine significantly attenuated oxidative stress and inflammatory reaction and increased interleukin-10 levels in cisplatin-induced intestinal mucositis ( < 0.05). Cisplatin administration resulted in high relative abundances of Deferribacteres and Proteobacteria and a low diversity of the microbiota when compared with control groups, D-methionine only and cisplatin plus D-methionine. Cisplatin markedly increased comparative abundances of and , while was almost completely depleted, compared with the control group. There were higher abundances of , Lachnospiraceae, and in cisplatin plus D-methionine rats than in cisplatin rats. D-methionine treatment alone significantly increased the number of .
CONCLUSION
D-methionine protects against cisplatin-induced intestinal damage through antioxidative and anti-inflammatory effects. By enhancing growth of beneficial bacteria (Lachnospiraceae and ), D-methionine attenuates gut microbiome imbalance caused by cisplatin and maintains gut homeostasis.
PubMed: 30792823
DOI: 10.1177/1758835918821021 -
Viruses Mar 2021Many bacteria carry bacteriophages (bacterial viruses) integrated in their genomes in the form of prophages, which replicate passively alongside their bacterial host....
Many bacteria carry bacteriophages (bacterial viruses) integrated in their genomes in the form of prophages, which replicate passively alongside their bacterial host. Environmental conditions can lead to prophage induction; the switching from prophage replication to lytic replication, that results in new bacteriophage progeny and the lysis of the bacterial host. Despite their abundance in the gut, little is known about what could be inducing these prophages. We show that several medications, at concentrations predicted in the gut, lead to prophage induction of bacterial isolates from the human gut. We tested five medication classes (non-steroidal anti-inflammatory, chemotherapy, mild analgesic, cardiac, and antibiotic) for antimicrobial activity against eight prophage-carrying human gut bacterial representative isolates in vitro. Seven out of eight bacteria showed signs of growth inhibition in response to at least one medication. All medications led to growth inhibition of at least one bacterial isolate. Prophage induction was confirmed in half of the treatments showing antimicrobial activity. Unlike antibiotics, host-targeted medications led to a species-specific induction of , , and to a lesser extent . These results show how common medication consumption can lead to phage-mediated effects, which in turn would alter the human gut microbiome through increased prophage induction.
Topics: Bacteria; Bacteriophages; Gastrointestinal Microbiome; Humans; Lysogeny; Pharmaceutical Preparations; Virus Activation
PubMed: 33799646
DOI: 10.3390/v13030455 -
Infection and Immunity Mar 2000Bacteria are a suspected pathogenic factor in inflammatory bowel disease, but the identity of the relevant microbial species remains unresolved. The pANCA autoantibody...
Bacteria are a suspected pathogenic factor in inflammatory bowel disease, but the identity of the relevant microbial species remains unresolved. The pANCA autoantibody is associated with most cases of ulcerative colitis (UC) and hence reflects an immune response associated with the disease process. This study addresses the hypothesis that pANCA identifies an antigen(s) expressed by bacteria resident in the human colonic mucosa. Libraries of colonic bacteria were generated using aerobic and anaerobic microbiologic culture conditions, and bacterial pools and clonal isolates were evaluated for cross-reactive antigens by immunoblot analysis using the pANCA monoclonal antibody Fab 5-3. Two major species of proteins immunoreactive to pANCA monoclonal antibodies were detected in bacteria from the anaerobic libraries. Colony isolates of the expressing bacteria were identified as Bacteroides caccae and Escherichia coli. Isolation and partial sequencing of the B. caccae antigen identified a 100-kDa protein without database homologous sequences. The E. coli protein was biochemically and genetically identified as the outer membrane porin OmpC. Enzyme-linked immunosorbent assay with human sera demonstrated elevated immunoglobulin G anti-OmpC in UC patients compared to healthy controls. These findings demonstrate that a pANCA monoclonal antibody detects a recurrent protein epitope expressed by colonic bacteria and implicates colonic bacterial proteins as a target of the disease-associated immune response.
Topics: Amino Acid Sequence; Antibodies, Antineutrophil Cytoplasmic; Autoantigens; Bacterial Proteins; Bacteroides; Colitis, Ulcerative; Colon; Cross Reactions; Epitopes; Escherichia coli; Humans; Molecular Sequence Data; Molecular Weight; Porins
PubMed: 10678972
DOI: 10.1128/IAI.68.3.1542-1548.2000 -
Genome Medicine May 2020Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo...
BACKGROUND
Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.
METHODS
We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.
RESULTS
During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.
CONCLUSIONS
We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.
Topics: Anti-Infective Agents; Azacitidine; Azithromycin; Bacteria; Ciprofloxacin; DNA, Bacterial; Diet; Feces; Gastrointestinal Microbiome; Genome, Bacterial; Hematopoietic Stem Cell Transplantation; Humans; Immunosuppressive Agents; Male; Metagenome; Middle Aged; Myelodysplastic Syndromes; Primary Myelofibrosis; RNA-Seq; Sequence Analysis, DNA
PubMed: 32471482
DOI: 10.1186/s13073-020-00747-0 -
Frontiers in Neuroscience 2020Attention-deficit/hyperactivity disorder (ADHD) is a neuropsychiatric condition that may be related to an imbalance of neural transmitters. The gut microbiota is the...
BACKGROUND
Attention-deficit/hyperactivity disorder (ADHD) is a neuropsychiatric condition that may be related to an imbalance of neural transmitters. The gut microbiota is the largest ecosystem in the human body, and the brain-gut axis theory proposes that the gut microbiome can affect brain function in multiple ways. The purpose of this study was to explore the gut microbiota in children with ADHD and assess the possible role of the gut microbiota in disease pathogenesis to open new avenues for ADHD treatment.
METHODS
A case-control design was used. We enrolled 17 children aged 6-12 years with ADHD who were treated in the Pediatric Outpatient Department of the First Medical Center of the Chinese PLA General Hospital from January to June, 2019. Seventeen children aged 6-12 years were selected as the healthy control (HC) group. Fecal samples of cases and controls were analyzed by shotgun metagenomics sequencing. Alpha diversity and the differences in the relative abundances of bacteria were compared between the two groups. Functional annotations were performed for the microbiota genes and metabolic pathways were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG).
RESULTS
There was no significant difference in the alpha diversity of gut microbiota between the ADHD and HC groups. Compared with HCs, and were significantly reduced in children with ADHD ( < 0.05), and were significantly increased [linear discriminant analysis (LDA) > 2]. At the species level, , , and were significantly reduced in the ADHD group ( < 0.05), while , , , and were increased ( < 0.05). Metabolic pathway analysis revealed significant between-group differences in the metabolic pathways of neurotransmitters (e.g., serotonin and dopamine) ( < 0.05).
CONCLUSION
Composition differences of gut microbiota in subjects with ADHD may contribute to brain-gut axis alterations and affect neurotransmitter levels, which could contribute to ADHD symptoms.
PubMed: 32132899
DOI: 10.3389/fnins.2020.00127 -
ISME Communications Mar 2021Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system...
Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.
PubMed: 36717704
DOI: 10.1038/s43705-021-00003-5