Biochemical Characterization of Two Rhamnogalacturonan Lyases From Bacteroides ovatus ATCC 8483 With Preference for RG-I Substrates

Rhamnogalacturonan lyase (RGL) cleaves backbone α-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acid residues in type I rhamnogalacturonan (RG-I) by β-elimination to generate RG oligosaccharides with various degrees of polymerization. Here, we cloned, expressed, purified and biochemically characterized two RGLs (Bo3128 and Bo4416) in the PL11 family from Bacteroides ovatus ATCC 8483. Bo3128 and Bo4416 displayed maximal activity at pH 9.5 and pH 6.5, respectively. Whereas the activity of Bo3128 could be increased 1.5 fold in the presence of 5 mM Ca2+, Bo4416 required divalent metal ions to show any enzymatic activity. Both of RGLs showed a substrate preference for RG-I compared to other pectin domains. Bo4416 and Bo3128 primarily yielded unsaturated RG oligosaccharides, with Bo3128 also producing them with short side chains, with yields of 32.4 and 62.4%, respectively. Characterization of both RGLs contribute to the preparation of rhamnogalacturonan oligosaccharides, as well as for the analysis of the fine structure of RG-I pectins.

Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus

With the knowledge of bacterial gene systems encoding proteins that target dietary carbohydrates as a source of nutrients and their importance for human health, major efforts are being made to understand carbohydrate recognition by various commensal bacteria. Here, we describe an integrative strategy that combines carbohydrate microarray technology with structural studies to further elucidate the molecular determinants of carbohydrate recognition by BoSGBP MLG -A, a key protein expressed at the surface of Bacteroides ovatus for utilization of mixed-linkage β1,3-1,4-glucans.

Rapidly Growing Aneurysm with Ulcer-like Projection Complicated with Bacteroides ovatus Bacteremia

The incidence of anaerobic bacteremia has been increasing over the past several decades. Further, antibiotic resistance in Bacteroides is a pertinent issue. A 76-year-old man was brought to our hospital with complaints of fever, chills, and abdominal pain. Empiric antibiotics induced minimal relief. The blood culture was positive for multi-drug resistant Bacteroides ovatus. Our patient developed a periaortic abscess in the abdominal aorta and a thoracic aortic aneurysm with ulcer-like projection (ULP), which rapidly increased in size. He was transferred to the tertiary medical institution for surgical drainage. This case suggests that bacteremia can exacerbate aneurysms with ulcerative lesions. Anaerobic bacteremia is a possible differential diagnosis when periaortic abscess formation is present. Early surgical consultation and appropriate antibiotic selection are crucial in anaerobic bacteremia treatment.

Immunoglobulin subtype-coated bacteria are correlated with the disease activity of inflammatory bowel disease

Immune response involving various immunoglobulin (Ig) isotypes and subtypes to microbiome is involved in the pathogenesis and disease activity of inflammatory bowel diseases (IBDs). To clarify the presence of Ig-coated bacteria in the intestine and its association with disease activity in ulcerative colitis (UC) and Crohn’s disease (CD), we extracted and classified Ig-coated bacteria from fecal samples of 42 patients with IBD and 12 healthy controls (HCs) using flow cytometry and 16S ribosomal RNA sequence analysis. The percentage of bacteria coated with IgA and IgM was higher in patients with IBD than in HCs, and IgG-coated bacteria were found only in patients with IBD. Moreover, the percentages of bacteria coated with IgG1, IgG2, IgG3, and IgM in UC samples and IgG3, IgG4, and IgM in CD samples were correlated with disease activities. The proportions of Bacteroides ovatus and Streptococcus increased during the active phase of CD. Hence, the detailed analysis of Ig-coated bacteria and Ig subtypes using flow cytometry could aid in developing useful indicators of disease activity and identifying more disease-related bacteria, which could become novel treatment targets for IBDs.

Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.

Intracellular Microbiome Profiling of the Acanthamoeba Clinical Isolates from Lens Associated Keratitis

Acanthamoeba act as hosts for various microorganisms and pathogens, causing Acanthamoeba Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a metagenomics study to characterize the intracellular microbiome from five lenses associated with AK isolates and standard strains to characterize the role of ocular flora in AK progression. The used clinical isolates were axenic cultured from lenses associated with AK patients. AK isolates and standard controls such as 16S ribosomal RNA sequencing techniques were used for analysis. The microbiome compositions and relative abundance values were compared. The orders of Clostridiales and Bacteroidales presented major populations of intracellular microbes belonging to all isolates. Comparison of the different source isolates showed that most of the abundance in keratitis isolates came from Ruminococcus gnavus (121.0 folds), Eubacterium dolichum (54.15 folds), Roseburia faecis (24.51 folds), and Blautia producta (3.15 folds). Further analysis of the relative abundance data from keratitis isolates showed that Blautia producta was positively correlated with the disease course. In contrast, Bacteroides ovatus was found to be abundant in early-stage keratitis isolates. This study reveals the abundant anaerobic Gram-positive rods present in severe keratitis isolate and characterize the association between Acanthamoeba and ocular flora in AK progression.

Author Correction: Prebiotic effects of yeast mannan, which selectively promotes Bacteroides thetaiotaomicron and Bacteroides ovatus in a human colonic microbiota model

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Fermentation of Ferulated Arabinoxylan Recovered from the Maize Bioethanol Industry

Maize by-product from the bioethanol industry (distiller’s dried grains with solubles, DDGS) is a source of ferulated arabinoxylan (AX), which is a health-promoting polysaccharide. In the present study, AX from DDGS was fermented by a representative colonic bacterial mixture (Bifidobacterium longum, Bifidobacterium adolescentis, and Bacteroides ovatus), and the effect of the fermented AX (AX-f) on the proliferation of the cell line Caco-2 was investigated. AX was efficiently metabolized by these bacteria, as evidenced by a decrease in the polysaccharide molecular weight from 209 kDa to < 50 kDa in AX-f, the release of ferulic acid (FA) from polysaccharide chains (1.14 µg/mg AX-f), and the short-chain fatty acids (SCFA) production (277 µmol/50 mg AX). AX-f inhibited the proliferation of Caco-2 cells by 80–40% using concentrations from 125–1000 µg/mL. This dose-dependent inverse effect was attributed to the increased viscosity of the media due to the polysaccharide concentration. The results suggest that the AX-f dose range and the SCFA and free FA production are key determinants of antiproliferative activity. Using the same polysaccharide concentrations, non-fermented AX only inhibited the Caco-2 cells proliferation by 8%. These findings highlight the potential of AX recovered from the maize bioethanol industry as an antiproliferative agent once fermented by colonic bacteria.