-
Nature Medicine Jun 2019In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition,...
In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition, accumulating evidence suggests that the human gut microbiome is linked to the development of colorectal cancer. Here we performed fecal metagenomic and metabolomic studies on samples from a large cohort of 616 participants who underwent colonoscopy to assess taxonomic and functional characteristics of gut microbiota and metabolites. Microbiome and metabolome shifts were apparent in cases of multiple polypoid adenomas and intramucosal carcinomas, in addition to more advanced lesions. We found two distinct patterns of microbiome elevations. First, the relative abundance of Fusobacterium nucleatum spp. was significantly (P < 0.005) elevated continuously from intramucosal carcinoma to more advanced stages. Second, Atopobium parvulum and Actinomyces odontolyticus, which co-occurred in intramucosal carcinomas, were significantly (P < 0.005) increased only in multiple polypoid adenomas and/or intramucosal carcinomas. Metabolome analyses showed that branched-chain amino acids and phenylalanine were significantly (P < 0.005) increased in intramucosal carcinomas and bile acids, including deoxycholate, were significantly (P < 0.005) elevated in multiple polypoid adenomas and/or intramucosal carcinomas. We identified metagenomic and metabolomic markers to discriminate cases of intramucosal carcinoma from the healthy controls. Our large-cohort multi-omics data indicate that shifts in the microbiome and metabolome occur from the very early stages of the development of colorectal cancer, which is of possible etiological and diagnostic importance.
Topics: Adult; Aged; Case-Control Studies; Colorectal Neoplasms; Disease Progression; Female; Gastrointestinal Microbiome; Humans; Male; Metabolomics; Metagenomics; Middle Aged; Neoplasm Staging; Young Adult
PubMed: 31171880
DOI: 10.1038/s41591-019-0458-7 -
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 -
Standards in Genomic Sciences Jun 2010
PubMed: 21304720
DOI: 10.4056/sigs.992408 -
Journal of Neuro-ophthalmology : the... Mar 2022Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade,...
BACKGROUND
Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity. Accordingly, we investigated whether the gut microbiome is modified in IIH patients compared with healthy controls, and provide possible new treatment venues.
METHODS
Shotgun metagenomic sequencing of the gut microbiome of 25 cases of IIH patients (according to the modified Dandy criteria) and 20 healthy controls. Participants were further stratified according to their body mass index. The total DNA from each sample was extracted using the PureLink Microbiome DNA Purification Kit A29789 (Invitrogen, Thermo Fisher Scientific, US). Library preparation was performed using the Nextera DNA Flex Library Prep Kit. Samples were sequenced on the Illumina Novaseq 6000 device. A list of bacterial species that significantly differed between the IIH patients and healthy controls was produced in addition to species diversity. In addition, patients' cohort alone was analyzed, (excluding the healthy controls), and the effect of acetazolamide treatment on their gut microbiota was analyzed.
RESULTS
IIH patients have a lower diversity of bacterial species compared with healthy individuals. These bacteria, that is, Lactobacillus ruminis (L. ruminis) (p<6.95E-08), Atopobium parvulum (p<3.9E-03), Megamonas hypermegale (p<5.61E-03), Ruminococcus gnavus (p<1.29E-02), MEL.A1 (p<3.04E-02), and Streptococcus sp. I-G2 (p<3.04E-02), were previously characterized with beneficial health effects. Moreover, we found that Lactobacillus brevis, a beneficial bacterium as well, is more abundant in acetazolamide treated patients (p<7.07E-06).
CONCLUSIONS
Gut microbiota plays a potential role in IIH etiology and therefore, can provide a promising new treatment approach for this disease.
Topics: Acetazolamide; Brain; Female; Gastrointestinal Microbiome; Humans; Obesity; Papilledema; Pseudotumor Cerebri
PubMed: 34270519
DOI: 10.1097/WNO.0000000000001330 -
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 -
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 -
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 -
Anaerobe Dec 2022We report an uncommon case of bacteremia due to Lancefieldella parvula isolated in pure culture. We present a 72 year-old-man affected with cancer admitted with...
We report an uncommon case of bacteremia due to Lancefieldella parvula isolated in pure culture. We present a 72 year-old-man affected with cancer admitted with abdominal pain due to a parietal rupture of the urinary bladder. After surgical treatment, the patient developed fever and two sets of blood cultures yielded a pure culture of an anaerobic microorganism identified as L. parvula (formerly Atopobium parvulum) by MALDI-TOF MS, and confirmed by 16S rRNA gene sequencing. The isolate was susceptible to all antibiotics and the outcome was finally successful. Bacteremia due to L. parvula is an uncommon disease and, in that case, MALDI-TOF MS was an useful tool for the initial identification.
Topics: Humans; Aged; RNA, Ribosomal, 16S; Bacteremia; Actinobacteria; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 36202324
DOI: 10.1016/j.anaerobe.2022.102661