Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques- a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)- degrades mucin glycoproteins or their component O -linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron . This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD.

Importance

An important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade different components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate particular species associated with bacterial mucus destruction and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another gut bacterium implicated in IBD, Bacteroides thetaiotaomicron . Our findings underscore the importance of understanding the mucin degradation mechanisms of different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately contribute to defects in mucus protection and could therefore be targets to prevent or treat IBD.

Breast Milk Oligosaccharides Contain Immunomodulatory Glucuronic Acid and LacdiNAc

Breast milk is abundant with functionalized milk oligosaccharides (MOs) to nourish and protect the neonate. Yet we lack a comprehensive understanding of the repertoire and evolution of MOs across Mammalia. We report ∼400 MO-species associations (>100 novel structures) from milk glycomics of nine mostly understudied species: alpaca, beluga whale, black rhinoceros, bottlenose dolphin, impala, L'Hoest's monkey, pygmy hippopotamus, domestic sheep, and striped dolphin. This revealed the hitherto unknown existence of the LacdiNAc motif (GalNAcβ1-4GlcNAc) in MOs of all species except alpaca, sheep, and striped dolphin, indicating the widespread occurrence of this potentially antimicrobial motif in MOs. We also characterize glucuronic acid-containing MOs in the milk of impala, dolphins, sheep, and rhinoceros, previously only reported in cows. We demonstrate that these GlcA-MOs exhibit potent immunomodulatory effects. Our study extends the number of known MOs by >15%. Combined with >1900 curated MO-species associations, we characterize MO motif distributions, presenting an exhaustive overview of MO biodiversity.

Intestinal mucus and their glycans: A habitat for thriving microbiota

The colon mucus layer is organized with an inner colon mucus layer that is impenetrable to bacteria and an outer mucus layer that is expanded to allow microbiota colonization. A major component of mucus is MUC2, a glycoprotein that is extensively decorated, especially with O-glycans. In the intestine, goblet cells are specialized in controlling glycosylation and making mucus. Some microbiota members are known to encode multiple proteins that are predicted to bind and/or cleave mucin glycans. The interactions between commensal microbiota and host mucins drive intestinal colonization, while at the same time, the microbiota can utilize the glycans on mucins and affect the colonic mucus properties. This review will examine this interaction between commensal microbes and intestinal mucins and discuss how this interplay affects health and disease.

Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota

Sulfated glycans are ubiquitous nutrient sources for microbial communities that have coevolved with eukaryotic hosts. Bacteria metabolize sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognize their glycan substrate remain poorly understood. Here, we use structural biology to determine how sulfatases from the human gut microbiota recognize sulfated glycans. We reveal seven new carbohydrate sulfatase structures spanning four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent novel structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity toward related but distinct glycan targets. Collectively, these data reveal that carbohydrate sulfatases are highly selective for the glycan component of their substrate. These data provide new approaches for probing sulfated glycan metabolism while revealing the roles carbohydrate sulfatases play in host glycan catabolism.

A single sulfatase is required to access colonic mucin by a gut bacterium

Humans have co-evolved with a dense community of microbial symbionts that inhabit the lower intestine. In the colon, secreted mucus creates a barrier that separates these microorganisms from the intestinal epithelium1. Some gut bacteria are able to utilize mucin glycoproteins, the main mucus component, as a nutrient source. However, it remains unclear which bacterial enzymes initiate degradation of the complex O-glycans found in mucins. In the distal colon, these glycans are heavily sulfated, but specific sulfatases that are active on colonic mucins have not been identified. Here we show that sulfatases are essential to the utilization of distal colonic mucin O-glycans by the human gut symbiont Bacteroides thetaiotaomicron. We characterized the activity of 12 different sulfatases produced by this species, showing that they are collectively active on all known sulfate linkages in O-glycans. Crystal structures of three enzymes provide mechanistic insight into the molecular basis of substrate specificity. Unexpectedly, we found that a single sulfatase is essential for utilization of sulfated O-glycans in vitro and also has a major role in vivo. Our results provide insight into the mechanisms of mucin degradation by a prominent group of gut bacteria, an important process for both normal microbial gut colonization2 and diseases such as inflammatory bowel disease3.

A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner

Efficient nutrient acquisition in the human gut is essential for microbial persistence. Although polysaccharides have been well-studied nutrients for the gut microbiome, other resources such as nucleic acids and nucleosides are less studied. We describe several ribose-utilization systems (RUSs) that are broadly represented in Bacteroidetes and appear to have diversified to access ribose from a variety of substrates. One Bacteroides thetaiotaomicron RUS variant is critical for competitive gut colonization in a diet-specific fashion. We used molecular genetics to probe the required functions of the system and the nature of the nutrient source(s) underlying this phenotype. Two RUS-encoded ribokinases were the only components required for this effect, presumably because they generate ribose-phosphate derivatives from products of an unlinked but essential nucleoside phosphorylase. Our results underscore the extensive mechanisms that gut symbionts have evolved to access nutrients and the potential for unexpected dependencies among systems that mediate colonization and persistence.

Bacteroides thetaiotaomicron

This infographic on Bacteroides thetaiotaomicron (Bt) explores the ability of this microbe to digest a broad array of complex carbohydrates, alter its surface features, and its emerging role in gastrointestinal diseases. The infographic of Bacteroides thetaiotaomicron (Bt) illustrates two key facets of its symbiotic lifestyle in the human gut: a broad ability to digest dietary fiber polysaccharides and host glycans, and a dynamic cell-surface architecture that promotes both interactions with and evasion of the host immune system. The starch-utilization system (Sus) is a cell-surface and periplasmic system involved in starch cleavage and transport. Over 80 additional Sus-like systems utilize substrates ranging from host glycans to plant cell wall pectins. Bt has evolved intricate strategies to interact with other microbes or its host, including modification of its surface. Some nutrient utilization pathways select for or directly trigger changes in capsular polysaccharide (CPS) expression. Like other fermentative members of the gut microbiome, Bt produces host absorbable short-chain and organic acids, which can all be absorbed by the host as a source of energy.

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes

Individual human gut bacteria often encode hundreds of enzymes for degrading different polysaccharides. Identification of co-localized and co-regulated genes in these bacteria has been a successful approach to identify enzymes that participate in full or partial saccharification of complex carbohydrates, often unmasking novel catalytic activities. Here, we review recent studies that have led to the discovery of new activities from gut bacteria and summarize a general scheme for identifying gut bacteria with novel catalytic abilities, locating the enzymes involved and investigating their activities in detail. The strength of this approach is amplified by the availability of abundant genomic and metagenomic data for the human gut microbiome, which facilitates comparative approaches to mine existing data for new or orthologous enzymes.

Corrigendum: Complex pectin metabolism by gut bacteria reveals novel catalytic functions

This corrects the article DOI: 10.1038/nature21725.

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

Carbohydrate polymers drive microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron utilizes the most structurally complex glycan known; the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but one of its 21 distinct glycosidic linkages. We show that rhamnogalacturonan-II side-chain and backbone deconstruction are coordinated, to overcome steric constraints, and that degradation reveals previously undiscovered enzyme families and novel catalytic activities. The degradome informs revision of the current structural model of RG-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycans in the human diet.

Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition

The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens The data identified six previously unidentified CBM families that targeted β-glucans, β-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize β-glucans and β-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose.

Endoscopic detachable mini-loop ligation for treatment of gastroduodenal angiodysplasia: case study of 11 patients with long-term follow-up

BACKGROUND

Detachable mini-loop ligation is useful for endoscopic management of esophageal varices. This study evaluated the treatment of gastroduodenal angiodysplasia by detachable mini-loop ligation.

METHODS

Eleven patients (9 women, 2 men; mean age 61 [18] years) with bleeding gastroduodenal angiodysplasia were treated endoscopically by detachable mini-loop ligation. At endoscopy, two patients had actively bleeding lesions. By using a ligating device, a detachable nylon ring was inserted through the accessory channel of an endoscope and opened at the rim of a transparent ligation chamber attached to the tip of the instrument. The angiodysplasia was aspirated into the chamber, and the mini-loop was closed and detached.

OBSERVATIONS

Initial ligation therapy was successful in all patients without inducing uncontrollable bleeding. In one patient, two mini-loops were applied to the same angiodysplastic lesion. The only significant complication was severe GI bleeding from a duodenal ulcer that developed at the ligation site in one patient. This was successfully treated by endoscopic placement of hemoclips.

CONCLUSIONS

Detachable mini-loop ligation is an effective and safe modality for endoscopic treatment of bleeding gastroduodenal angiodysplasia.

Tissue Doppler imaging in different locations of the mitral annulus: all different or all the same?

BACKGROUND

The assessment of the mitral annulus motion with tissue Doppler imaging is claimed to be an accurate method to quantify global left ventricular systolic and diastolic function. However, it is not yet perfectly defined which site of the annulus must be selected. Familial amyloidotic polyneuropathy of the Portuguese type (FAP) is an hereditary systemic disease in which diastolic dysfunction may occur.

AIM

1--To determine if in FAP patients the mitral annulus motion is independent of the selected site. 2--To compare pulsed wave Doppler parameters with tissue Doppler parameters in the different annular sites.

METHODS

Of 24 FAP patients studied, 14 were included. In each patient we performed conventional transmitral pulsed wave Doppler and tissue Doppler in the 4 sites of the mitral annulus and measured the velocities of the rapid filling wave e, of the atrial contraction wave a and calculated e/a ratio.

RESULTS

According to the transmitral inflow profile, patients were divided in 2 groups: Group I--normal global diastolic function and Group II--abnormal relaxation. Group I--33% of these patients showed e/a > 1 in the four sites and 67% showed e/a > 1 in at least 1, but not in all the sites. The rate of normal sites per patient was 3.1. Group II--25% of these patients showed e/a < 1 in the 4 sites of the annulus and 75% had e/a < 1 in at least 1, but not in all the sites analysed. The rate of abnormal sites/patient was 3.1. in this group. When conventional and tissue Doppler data were compared (bland and altman) the septal portion of the annulus was the one with the best correlation.

CONCLUSIONS

1--The assessment of the mitral annulus motion with tissue Doppler imaging is dependent on the site selected for study. 2--The septal site was the one that showed the highest correlation and concordance between pulsed wave Doppler and tissue Doppler. 3--The relative number of normal versus abnormal sites was determinant of the transmitral pattern. 4--Tissue Doppler imaging identified: a) among patients until now classified as normal diastolic function, a subgroup of patients with abnormal function in some sites of the annulus and b) among patients with abnormal relaxation, a subgroup with normal diastolic function in some sites of the annulus.

DNA binding alkaloids from Prosopis alba

The known beta-phenethylamine ( 1) and the new alkaloid 2-beta-methyl-3-beta-hydroxy-6-beta-piperidinedodecanol ( 2) were isolated from the aerial parts of PROSOPIS ALBA. Both compounds showed DNA binding effects of 27 and 50%, respectively, at 0.50 mg/ml.

[Homocysteinemia as a risk factor for cerebrovascular disorders. The role of age and homocysteine levels]

PURPOSE

To evaluate importance of homocysteinemia as risk factor of thrombotic cerebrovascular disease, in terms of age and homocysteinemia levels.

METHODS

A group of patients under 55 years old (n = 35, 21 males) that had suffered a stroke 3 months to 1 year before the study, defined by clinical criteria and the presence of cerebral infarction confirmed by tomography, without history or predisponents to embolic disease. The patients were matched with a group of controls without vascular pathology of a check-up program, in terms of age and sex. Patients and controls with history of alcoholism, signs or laboratory of renal or hepatic insufficiency or with history of recent ingestion of vitamins of the group B were excluded since these conditions could influence homocysteinemia levels. We measured to patients and controls the plasmatic basal homocysteinemia and homocysteinemia 6 hours after methionine overload of 0.1 g/Kg body weigh. We estimated case-control odds ratio of hyperhomocysteinemia globally and by age groups, and odd ratio of different levels of homocysteinemia.

RESULTS AND CONCLUSIONS

Hyperhomocysteinemia case-control global odds ratio was 5.7, being higher in younger patients (8.8 below and 3.5 after the age of 45 years). Homocysteinemia as a risk factor of cerebrovascular disease presented as a continuous effect: low homocysteinemia was protective, and the higher the homocysteinemia, the higher the cerebrovascular risk proved to be. In these circumstances, heterozygozyty of cysthationine beta synthase deficiency, refered as the more important cause of hyperhomocysteinemia, cannot account for most of the cases of hyperhomocysteinemia.

Homocysteinaemia after methionine overload as a coronary artery disease risk factor: importance of age and homocysteine levels

BACKGROUND

Homocysteinaemia is now accepted as an independent risk factor for coronary artery disease (CAD). Our goal was to study the influence of age plasma homocysteine level on the CAD risk attributable to homocysteinaemia.

METHODS

We studied a group of 98 patients under 55 years of age who had suffered a myocardial infarction 3-12 months before the study. The patients were matched by sex and age with a group of 98 controls without vascular disease. We measured the plasma homocysteine levels 6h after a methionine overload of 0.1 g/kg body weight in patients and controls. Afterwards, the odds ratio for homocysteinaemia was determined by homocysteine level, and that for hyperhomocysteinaemia (homocysteine level > 34 mumol/l) by age group.

RESULTS

After methionine loading, the homocysteine odds ratio varied from 0.47 (homocysteine level < 23 mumol/l) to 2.88 (homocysteine level > 34 mumol/l). In patients under the age of 46 the odds ratio for hyperhomocysteinaemia was 18.6. In patients between 46 and 55 years of age the odds ratio for hyperhomocysteinaemia was 1.2.

CONCLUSIONS

Low homocysteine levels are protective against CAD, and the higher the homocysteine level the higher the coronary risk appears to be. This clearly means that heterozygosity for cystathionine beta synthase deficiency alone is not enough to explain the vascular risk associated with homocysteinaemia. Hyperhomocysteinemia was shown to be a significant risk factor only in patients under the age of 46 years old.