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FEBS Letters Apr 2022Crohn's disease (CD) is characterized by the chronic inflammation of the gastrointestinal tract. A dysbiotic microbiome and a defective immune system are linked to CD,...
Crohn's disease (CD) is characterized by the chronic inflammation of the gastrointestinal tract. A dysbiotic microbiome and a defective immune system are linked to CD, where hydrogen sulfide (H S) microbial producers positively correlate with the severity of the disease. Atopobium parvulum is a key H S producer from the microbiome of CD patients. In this study, the biochemical characterization of two Atopobium parvulum cysteine desulfurases, ApSufS and ApCsdB, shows that the enzymes are allosterically regulated. Structural analyses reveal that ApSufS forms a dimer with conserved characteristics observed in type II cysteine desulfurases. Four residues surrounding the active site are essential to catalyse cysteine desulfurylation, and a segment of short-chain residues grant access for substrate binding. A better understanding of ApSufS will help future avenues for CD treatment.
Topics: Actinobacteria; Carbon-Sulfur Lyases; Crohn Disease; Cysteine; Humans
PubMed: 35122247
DOI: 10.1002/1873-3468.14295 -
Standards in Genomic Sciences Sep 2009Atopobium parvulum (Weinberg et al. 1937) Collins and Wallbanks 1993 comb. nov. is the type strain of the species and belongs to the genomically yet unstudied...
Atopobium parvulum (Weinberg et al. 1937) Collins and Wallbanks 1993 comb. nov. is the type strain of the species and belongs to the genomically yet unstudied Atopobium/Olsenella branch of the family Coriobacteriaceae. The species A. parvulum is of interest because its members are frequently isolated from the human oral cavity and are found to be associated with halitosis (oral malodor) but not with periodontitis. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Atopobium, and the 1,543,805 bp long single replicon genome with its 1369 protein-coding and 49 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
PubMed: 21304653
DOI: 10.4056/sigs.29547 -
Nature Communications Nov 2016Intestinal microbial dysbiosis is associated with Crohn's disease (CD). However, the mechanisms leading to the chronic mucosal inflammation that characterizes this...
Intestinal microbial dysbiosis is associated with Crohn's disease (CD). However, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. In this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. We report an altered host proteome in CD patients indicative of impaired mitochondrial functions. In particular, mitochondrial proteins implicated in HS detoxification are downregulated, while the relative abundance of HS microbial producers is increased. Network correlation analysis reveals that Atopobium parvulum controls the central hub of HS producers. A. parvulum induces pancolitis in colitis-susceptible interleukin-10-deficient mice and this phenotype requires the presence of the intestinal microbiota. Administrating the HS scavenger bismuth mitigates A. parvulum-induced colitis in vivo. This study reveals that host-microbiota interactions are disturbed in CD and thus provides mechanistic insights into CD pathogenesis.
Topics: Adolescent; Animals; Bacteria; Child; Child, Preschool; Crohn Disease; Female; Gastrointestinal Microbiome; Germ-Free Life; Humans; Interleukin-10; Male; Mice; Mice, Knockout; Phylogeny
PubMed: 27876802
DOI: 10.1038/ncomms13419 -
Beijing Da Xue Xue Bao. Yi Xue Ban =... Feb 2018To investigate the characterization of the salivary microbiome in people with obesity and the differences in microbial composition, gene function and metabolic pathways...
OBJECTIVE
To investigate the characterization of the salivary microbiome in people with obesity and the differences in microbial composition, gene function and metabolic pathways of salivary microbiome between people with obesity and normal weight controls.
METHODS
The study was carried out in people with obesity and age- and sex-matched normal weight controls. None of these selected participants had the systemic disease, oral mucosal disease or periodontal disease. Unstimulated saliva samples were collected and oral examination was conducted. DNAs from saliva samples were extracted and sequenced in an Illumina NextSeq 500 platform. Community composition, linear discriminant analysis of taxonomic differences,gene prediction, gene set construction and annotation of gene function were performed.
RESULTS
The classified bacterial reads of the samples were 2 630 428 for each sample. A total of 11 phyla, 19 classes, 26 orders, 41 families, 62 genera and 164 species were detected ultimately. All samples had the same predominant phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria). There were statistical differences between the groups at the class, order, family, genus and species levels. At the class level, Negativicutes and Erysipelotrichia were more abundant in the obesity group, while Flavobacteriia and Bateroidetes dominated in normal weight group (P<0.05). At the species level, 16 showed significant differences in relative abundance among the groups, in which Prevotella melaninogenica,Prevotella salivae,Solobacterium moorei and Atopobium parvulum ware more abundant in the obesity group, whereas Streptococcus sanguinis dominated in normal weight group (P<0.05). The people with obesity had a higher number of salivary microbial genes (P<0.05). We produced statistics on gene prediction and found salivary microbiome of obesity group had a higher number of genes (P < 0.05). Genes associated with the pathways of metabolism and environmental information processing and human diseases were significantly enriched in the saliva samples of people with obesity (P < 0.01).
CONCLUSION
Significant differences were seen in composition, gene function and metabolic pathways of salivary microbiome between people with obesity and normal weight people. We hope to go on further study with larger sample size in the near future.
Topics: Bacteria; Female; Humans; Male; Microbiota; Obesity; Pilot Projects; RNA, Ribosomal, 16S; Saliva
PubMed: 29483715
DOI: No ID Found -
Microorganisms Mar 2020The gut microbiota may have an impact on obesity. To date, the majority of studies in obese patients reported microbiota composition in stool samples. The aim of this...
The gut microbiota may have an impact on obesity. To date, the majority of studies in obese patients reported microbiota composition in stool samples. The aim of this study was to investigate the duodenal mucosa dysbiosis in adult obese individuals from Campania, a region in Italy with a very high percentage of obese people, to highlight microbial taxa likely associated with obesity. Duodenum biopsies were taken during upper gastrointestinal endoscopy in 19 obese (OB) and 16 lean control subjects (CO) and microbiome studied by 16S rRNA gene sequencing. Duodenal microbiome in our groups consisted of six phyla: Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Proteobacteria (51.1% vs. 40.1%) and Firmicutes (33.6% vs. 44.9%) were significantly ( < 0.05) more and less abundant in OB compared with CO, respectively. , and were reduced ( < 0.01) and Pseudomonadales were increased ( < 0.05) in OB compared with CO. Receiver operating characteristic curve analysis showed Atopobium and Oribacterium genera able to discriminate with accuracy (power = 75% and 78%, respectively) OB from CO. In conclusion, increased Proteobacteria and decreased Firmicutes (Lachnospiraceae) characterized the duodenal microbiome of obese subjects. These data direct to further studies to evaluate the functional role of the dysbiotic-obese-associated signature.
PubMed: 32235377
DOI: 10.3390/microorganisms8040485 -
Journal of Oral Microbiology 2022Severe-early childhood caries (S-ECC) a global problem of significant concern, commonly manifest on the occlusal, and proximal surfaces of affected teeth. Despite the...
BACKGROUND
Severe-early childhood caries (S-ECC) a global problem of significant concern, commonly manifest on the occlusal, and proximal surfaces of affected teeth. Despite the major ecological differences between these two niches the compositional differences, if any, in the microbiota of such lesions is unknown.
METHODS
Deep-dentine caries samples from asymptomatic primary molars of children with S-ECC (n 19) belonging to caries-code 5/6, (ICDAS classification) were evaluated. Employing two primer pools, we amplified and compared the bacterial gene sequences of the seven hypervariable regions (V2-V4 and V6-V9) using NGS-based assay.
RESULTS
Bray-Curtisevaluation indicated that occlusal lesions (OL) had a more homogeneous community than the proximal lesions (PL) with significant compositional differences at the species level ( = 0.01; R- 0.513). Together, the occlusal and proximal niches harbored 263 species, of which 202 (76.8%) species were common to both , while 49 (18.6%) and 12 (4.6%) disparate species were exclusively isolated from the proximal and occlusal niches, respectively. The most commonl genera at both niches included , and was predominant in PL ( ≤ 0.05), and ( = 0.01) was predominant in OL.
CONCLUSIONS
Distinct differences exist between the caries microbiota of occlusal and proximal caries in S-ECC.
PubMed: 35173909
DOI: 10.1080/20002297.2022.2037832 -
PloS One 2018Oral administration of hydrogen water ameliorates Parkinson's disease (PD) in rats, mice, and humans. We previously reported that the number of putative...
Oral administration of hydrogen water ameliorates Parkinson's disease (PD) in rats, mice, and humans. We previously reported that the number of putative hydrogen-producing bacteria in intestinal microbiota is low in PD compared to controls. We also reported that the amount of hydrogen produced by ingestion of lactulose is low in PD patients. The decreased hydrogen production by intestinal microbiota may be associated with the development and progression of PD. We measured the amount of hydrogen production using gas chromatography by seven bacterial strains, which represented seven major intestinal bacterial groups/genera/species. Blautia coccoides and Clostridium leptum produced the largest amount of hydrogen. Escherichia coli and Bacteroides fragilis constituted the second group that produced hydrogen 34- to 93-fold lower than B. coccoides. Bifidobacterium pseudocatenulatum and Atopobium parvulum constituted the third group that produced hydrogen 559- to 2164-fold lower than B. coccoides. Lactobacillus casei produced no detectable hydrogen. Assuming that taxonomically neighboring strains have similar hydrogen production, we simulated hydrogen production using intestinal microbiota that we previously reported, and found that PD patients produce a 2.2-fold lower amount of intestinal hydrogen compared to controls. The lower amount of intestinal hydrogen production in PD was also simulated in cohorts of two other countries. The number of hydrogen-producing intestinal bacteria may be associated with the development and progression of PD. Further studies are required to prove its beneficial effect.
Topics: Bacteria; Case-Control Studies; Feces; Gastrointestinal Microbiome; Humans; Hydrogen; Parkinson Disease; Time Factors
PubMed: 30586410
DOI: 10.1371/journal.pone.0208313 -
Journal of Oral Microbiology 2022The oral microbiota plays vital roles in both oral and systemic health, but limited studies have explored the transition of the female oral microbiota from preconception...
BACKGROUND
The oral microbiota plays vital roles in both oral and systemic health, but limited studies have explored the transition of the female oral microbiota from preconception to pregnancy along with pronounced hormonal fluctuations.
AIM
To characterize the oral microbiota among women in preconception and pregnancy through a prospective study and to explore the associations between the oral microbiota and oral hygiene practices.
METHODS
A total of 202 unstimulated saliva samples were collected from 101 women in both preconception and late pregnancy. The oral microbiota was analyzed using gene sequencing.
RESULTS
The Ace and phylogenetic diversity (PD) index were significantly lower in the third trimester than preconception. The pathogenic taxa and were significantly higher during late pregnancy than preconception. Women with overall better oral hygiene practice showed lower richness and diversity in preconception compared to women with poorer oral hygiene practice. The abundance of pathogens such as during both preconception and pregnancy decreased among women with better oral hygiene practice.
CONCLUSIONS
The composition of the oral microbiota changed slightly from preconception to late pregnancy, with more pathogens in saliva samples during pregnancy. Improving oral hygiene practices has the potential to maintain oral micro-ecological balance.
PubMed: 35341210
DOI: 10.1080/20002297.2022.2053389 -
Journal of Clinical Medicine Jun 2022One promising research trend involves evaluating the influence of microbiota in the reproductive system of women on becoming pregnant and maintaining pregnancy. The goal...
One promising research trend involves evaluating the influence of microbiota in the reproductive system of women on becoming pregnant and maintaining pregnancy. The goal of this study was to define the microflora profile of the endometrium and uterine cervix in women qualified for an in vitro fertilization (IVF) procedure, which is expected to contribute to increasing the percentage of successful IVF implantations. Based on the conducted molecular analysis in the collected swabs, 22 bacterial strains were identified. Eleven strains (57%) that were isolated belong to the physiological microflora, the most common strain of which was Lactobacillus. Eight of the isolated strains (33%) were pathological microflora, among which the most common bacteria were from the Enterobacteriaceae family (which includes E. coli, Shigella, and Salmonella). Finally, three of the bacterial strains (10%) may be a component of both physiological or pathological microflora of the vagina: Bifidobacterium breve, Bifidobacterium longum group, and Alloscardovia omnicolens. The presence of Escherichia coli was detected in six women, Staphylococcus aureus also in six patients, Atopobium parvulum in three, Streptococcus salivarius group in three, Enterococcus faecalis in four, and Aerococcus christensenii in two patients. We found statistically significant relationships (p < 0.05) between Lactobacillus fermentum and Enterococcus faecalis, Lactobacillus delbrueckii and Escherichia coli groups, Lactobacillus FN667084_s and Staphylococcus aureus groups, as well as Lactobacillus fermentum and Streptococcus agalactiae. Based on the conducted study, it may be confirmed that the endometrium is, to a large extent, colonized by lactic acid bacilli. Apart from that, endometrial dysbiosis was not noted in patients qualified for the IVF procedure.
PubMed: 35743414
DOI: 10.3390/jcm11123348 -
Standards in Genomic Sciences Jun 2010
PubMed: 21304720
DOI: 10.4056/sigs.992408