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Journal of Clinical Microbiology Dec 2004Two groups of unknown bacteria, which phenotypically resemble members of the Bacteroides fragilis group but phylogenetically display >5% 16S rRNA gene sequence...
Two groups of unknown bacteria, which phenotypically resemble members of the Bacteroides fragilis group but phylogenetically display >5% 16S rRNA gene sequence divergence from their nearest validly described species, Bacteroides thetaiotaomicron, were characterized by phenotypic and molecular taxonomic methods. Phylogenetically and phenotypically, the unidentified bacteria displayed a relatively close association with each other. However, a 16S rRNA gene sequence divergence of approximately 4% between the two unknown bacteria, as well as distinguishable biochemical characteristics, demonstrates that these organisms are genotypically and phenotypically distinct, and each group may represent a previously unknown subline within the Bacteroides phylogenetic cluster. Subsequent DNA-DNA hybridization studies confirmed that the two novel organisms were indeed distinct from each other. The previously described species closest to both of them is B. thetaiotaomicron (approximately 94% sequence similarity), but they can be differentiated easily from B. thetaiotaomicron by virtue of not utilizing trehalose. DNA-DNA pairing studies also documented the separateness of the unknown species and B. thetaiotaomicron. Based on the phenotypic and phylogenetic findings, two new species, "Bacteroides nordii" sp. nov. and "Bacteroides salyersae" sp. nov, are proposed. The G+C content of the DNA is 41.4 mol% for Bacteroides nordii and 42.0 mol% for Bacteroides salyersae. The type strains of Bacteroides nordii and Bacteroides salyersae are WAL 11050 (ATCC BAA-998 or CCUG 48943) and WAL 10018 (ATCC BAA-997 or CCUG 48945), respectively.
Topics: Bacterial Typing Techniques; Bacteroides; Bacteroides Infections; Fatty Acids; Humans; Intestines; Molecular Sequence Data; Nucleic Acid Hybridization; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 15583282
DOI: 10.1128/JCM.42.12.5565-5570.2004 -
Novel Thermostable Heparinase Based on the Genome of Bacteroides Isolated from Human Gut Microbiota.Foods (Basel, Switzerland) May 2022Among the nutrients available to the human gut microbiota, the complex carbohydrates and glycosaminoglycans are important sources of carbon for some of the species of...
Among the nutrients available to the human gut microbiota, the complex carbohydrates and glycosaminoglycans are important sources of carbon for some of the species of human gut microbiota. Glycosaminoglycan (heparin) from the host is a highly preferred carbohydrate for . To explore how gut microbiota can effectively use heparin as a carbon source for growth, we conducted a screening of the Carbohydrate-Active enzymes (CAZymes) database for lytic enzymes of the PL13 family and Research Center of Food Biotechnology at School of Food Science and Technology of Jiangnan University database of to identify novel glycosaminoglycan-degrading bacterial strains. Four species (, , , and ) that degraded heparin were selected for further studies. Analysis of the polysaccharide utilization sites of the four strains revealed that all of them harbored enzyme encoding genes of the PL13 family. Functional analysis revealed the activity of CAZymes in a medium containing heparin as the sole carbon source, suggesting their potential to degrade heparin and support growth. The four enzymes were heterologous expressed, and their enzymatic properties, kinetics, and thermal stability were determined. The lytic enzyme of had high enzymatic activity and thermal stability. The features that cause this high thermal stability were elucidated based on an examination of the three-dimensional structure of the protein. Our findings provide an important theoretical basis for the application of glycosaminoglycans and glycosaminoglycan-degrading enzymes in the medical and biotechnology industries, and an important scientific basis for precision nutrition and medical intervention studies using gut microbiota or enzymes as targets.
PubMed: 35627031
DOI: 10.3390/foods11101462 -
Annals of Translational Medicine Jun 2023Type 2 diabetes mellitus (T2DM) is a risk factor for acute myocardial infarction (AMI) and a common comorbidity in patients with AMI. T2DM doubles the fatality rate of...
BACKGROUND
Type 2 diabetes mellitus (T2DM) is a risk factor for acute myocardial infarction (AMI) and a common comorbidity in patients with AMI. T2DM doubles the fatality rate of patients with AMI in the acute phase of AMI and the follow-up period. However, the mechanisms by which T2DM increases the fatality rate remain unknown. This study sought to investigate changes in the gut microbiota of patients with AMI and T2DM (AMIDM) to extend understandings of the relative mechanisms from the aspects of gut microbiota.
METHODS
Patients were recruited and divided into 2 groups comprising 15 patients with AMIDM and 15 patients with AMI but without T2DM (AMINDM). Their stool samples and clinical information were collected. 16S ribosomal DNA sequencing was used to analyze the structure and composition of the gut microbiota based on the operational taxonomic units.
RESULTS
A significant difference was observed in the gut microbiota β diversity between the 2 groups. At the phylum level, the AMIDM patients showed an increase in the abundance of and a decrease in the abundance of compared to the AMINDM patients. At the genus level, the AMIDM patients showed an increase in the abundance of , and , and a decrease in the abundance of and compared to the AMINDM patients. At the species level, the AMIDM patients showed an increase in the abundance of species unclassified group, , , unclassified , uncultured , , , , , unclassified , and the group compared to the AMINDM patients. The gut microbiota function predictions indicated that the nucleotide metabolism-related pathway was significantly more increase in the patients with AMIDM than those with AMINDM. Additionally, the patients with AMIDM showed an increase in gram-positive bacteria and a decrease in the proportion of gram-negative bacteria. Our correlation analysis results on the gut microbiota and clinical parameters might extend understandings of the progression of AMI.
CONCLUSIONS
Changes in the gut microbiota composition of patients with AMIDM affect the severity of the metabolic disturbance and may be responsible for poorer clinical outcomes and worse disease progression in patients with AMIDM compared to those with AMINDM.
PubMed: 37405000
DOI: 10.21037/atm-22-3521 -
BMC Medicine Jan 2022COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies...
BACKGROUND
COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology.
METHODS
To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients.
RESULTS
Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients.
CONCLUSIONS
Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.
Topics: COVID-19; Dysbiosis; Gastrointestinal Microbiome; Homeostasis; Humans; SARS-CoV-2
PubMed: 35045853
DOI: 10.1186/s12916-021-02212-0 -
Nutrients Jan 2023A controlled-neonatal piglet trial was conducted to evaluate the impact of a plant-based infant formula containing buckwheat and almonds as the main source of protein...
Evaluation of a Plant-Based Infant Formula Containing Almonds and Buckwheat on Gut Microbiota Composition, Intestine Morphology, Metabolic and Immune Markers in a Neonatal Piglet Model.
A controlled-neonatal piglet trial was conducted to evaluate the impact of a plant-based infant formula containing buckwheat and almonds as the main source of protein compared to a commercially available dairy-based formula on the gut health parameters. Two day old piglets were fed either a plant-based or a dairy-based formula until day 21. Gut microbiome, cytokines, growth and metabolism related outcomes, and intestinal morphology were evaluated to determine the safety of the plant-based infant formula. This study reported that the plant-based formula-fed piglets had a similar intestinal microbiota composition relative to the dairy-based formula-fed group. However, differential abundance of specific microbiota species was detected within each diet group in the small and large intestinal regions and fecal samples. Lactobacillus delbrueckii, Lactobacillus crispatus, and Fusobacterium sp. had higher abundance in the small intestine of plant-based formula-fed piglets compared to the dairy-based group. Bacteroides nordii, Enterococcus sp., Lactobacillus crispatus, Prevotella sp., Ruminococcus lactaris, Bacteroides nordii, Eisenbergiella sp., Lactobacillus crispatus, Prevotella sp., and Akkermansia muciniphila had greater abundance in the large intestine of the plant based diet fed piglets relative to the dairy-based diet group. In the feces, Clostridiales, Bacteroides uniformis, Butyricimonasvirosa, Cloacibacillus porcorum, Clostridium clostridioforme, and Fusobacterium sp. were abundant in dairy-based group relative to the plant-based group. Lachnospiraceae, Clostridium scindens, Lactobacillus coleohominis, and Prevetolla sp. had greater abundance in the feces of the plant-based group in comparison to the dairy-based group. Gut morphology was similar between the plant and the dairy-based formula-fed piglets. Circulatory cytokines, magnesium, triiodothyronine (T3), thyroxine (T4), thyroid stimulating hormone (TSH), vitamin D, vitamin K, and IgE levels were similar among all piglets independent of dietary group. Overall, the present study demonstrated that a plant-based formula with buckwheat and almonds as the primary source of protein can support similar gut microbiota growth and health outcomes compared to a dairy-based infant formula.
Topics: Animals; Animals, Newborn; Biomarkers; Cytokines; Fagopyrum; Gastrointestinal Microbiome; Infant Formula; Intestine, Small; Prunus dulcis; Swine
PubMed: 36678256
DOI: 10.3390/nu15020383 -
International Journal of Medical... Aug 2022The emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat...
INTRODUCTION
The emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat to human health. However, knowledge on the diversity of the multidrug-resistant strains and the genetic elements carrying the antibiotic resistance genes (ARGs) remains limited.
AIM
The objective of the study was to describe the resistome in cfiA-positive B. fragilis.
METHODS
A collection of cfiA-positive B. fragilis from diverse human (8 bacteremias, 15 wound infections) and animal (2 chickens, 2 pigs, 6 dogs, 3 cats) sources in Hong Kong, 2015-2017 was analysed by whole genome sequencing.
RESULTS
In the 36 isolates, 13 distinct ARGs (total number 83, median 2, range 0-7 per isolate) other than cfiA were detected. ARGs encoding resistance to aminoglycosides, β-lactams, macrolides, sulphonamides and tetracyclines were carried by CTn341-like, CTnHyb-like, Tn5220-like, Tn4555-like and Tn613-like transposons and were detected in phylogenetically diverse isolates of different host sources. Only few ARGs encoding resistance to metronidazole and tetracyclines were localized on plasmids. In two chicken isolates, a novel transposon (designated as Tn6994) was found to be involved in the dissemination of multiple ARGs mediating resistance to multiple antibiotics, including metronidazole and linezolid that are critically important for treatment of anaerobic infections. In mating experiments, Tn6994 and the associated phenotypic resistance could be transferred to Bacteroides nordii recipient.
CONCLUSION
This study illustrates the importance of transposons in the dissemination of ARGs in the cfiA-positive division of B. fragilis. One Health approach is necessary to track the dissemination of ARGs.
Topics: Aminoglycosides; Animals; Anti-Bacterial Agents; Bacterial Infections; Bacterial Proteins; Bacteroides Infections; Bacteroides fragilis; Chickens; Dogs; Drug Resistance, Microbial; Humans; Linezolid; Macrolides; Metronidazole; Microbial Sensitivity Tests; Phylogeny; Sulfonamides; Swine; Tetracyclines; Whole Genome Sequencing; beta-Lactamases; beta-Lactams
PubMed: 35961233
DOI: 10.1016/j.ijmm.2022.151559 -
Journal of Medical Microbiology Jun 2020. Ankylosing spondylitis (AS) is a systemic progressive disease with an unknown etiology that may be related to the gut microbiome. Therefore, a more thorough...
Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment.
. Ankylosing spondylitis (AS) is a systemic progressive disease with an unknown etiology that may be related to the gut microbiome. Therefore, a more thorough understanding of its pathogenesis is necessary for directing future therapy.. We aimed to determine the differences in intestinal microbial composition between healthy individuals and patients with AS who received and who did not receive treatment interventions. In parallel, the pathology of AS in each patient was analysed to better understand the link between AS treatment and the intestinal microbiota of the patients.. Sixty-six faecal DNA samples, including 37 from healthy controls (HCs), 11 from patients with untreated AS (NM), 7 from patients treated with nonsteroidal anti-inflammatory drugs (e.g. celecoxib; WM) and 11 from patients treated with Chinese herbal medicine (CHM), such as the Bushen-Qiangdu-Zhilv decoction, were collected and used in the drug effect analysis. All samples were sequenced using Illumina HiSeq 4000 and the microbial composition was determined.. Four species were enriched in the patients with AS: , , and (HC vs. NM, <0.05); only was found to be significantly changed in the NM-HC comparison. No additional species were found in the HC vs. CHM analysis, which indicated a beneficial effect of CHM in removing the other three strains. was found to be significantly increased in the comparison between the HC and WM groups, along with four other species (, Clostridiales bacterium 1_7_47FAA, and ). The patients with AS harboured more bacterial species associated with carbohydrate metabolism and glycan biosynthesis in their faeces. They also had bacterial profiles less able to biodegrade xenobiotics or synthesize and transport vitamins.. The gut microbiota of the patients with AS varied from that of the HCs, and the treatment had an impact on this divergence. Our data provide insight that could guide improvements in AS treatment.
Topics: Adolescent; Adult; Drugs, Chinese Herbal; Dysbiosis; Gastrointestinal Microbiome; Humans; Metagenome; Middle Aged; Spondylitis, Ankylosing; Young Adult
PubMed: 31778109
DOI: 10.1099/jmm.0.001107