Microbiome of root vegetables—a source of gluten-degrading bacteria

Gluten is a cereal protein that is incompletely digested by human proteolytic enzymes that create immunogenic peptides that accumulate in the gastrointestinal tract (GIT). Although both environmental and human bacteria have been shown to expedite gluten hydrolysis, gluten intolerance is a growing concern. Here we hypothesize that together with food, we acquire environmental bacteria that could impact our GIT with gluten-degrading bacteria. Using in vitro gastrointestinal simulation conditions, we evaluated the capacity of endophytic bacteria that inhabit root vegetables, potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), and topinambur (Jerusalem artichoke) (Helianthus tuberosus), to resist these conditions and degrade gluten. By 16S rDNA sequencing, we discovered that bacteria from the families Enterobacteriaceae, Bacillaceae, and Clostridiaceae most effectively multiply in conditions similar to the human GIT (microoxic conditions, 37 °C) while utilizing vegetable material and gluten as nutrients. Additionally, we used stomach simulation (1 h, pH 3) and intestinal simulation (1 h, bile salts 0.4%) treatments. The bacteria that survived this treatment retained the ability to degrade gluten epitopes but at lower levels. Four bacterial strains belonging to species Bacillus pumilus, Clostridium subterminale, and Clostridium sporogenes isolated from vegetable roots produced proteases with postproline cleaving activity that successfully neutralized the toxic immunogenic epitopes. Key points • Bacteria from root vegetables can degrade gluten. • Some of these bacteria can resist conditions mimicking gastrointestinal tract.

Antioxidants maintain Butyrate production by Human GutClostridiain the presence of Oxygen

ABSTRACTBackgroundOxygen diffused from the human gut mucosa and shape the microbiota with a radial gradient of microbes according to their oxygen tolerance, while microbial and chemical oxygen consumption maintains the lumen in a deeply anaerobic state. Uncontrolled oxidative stress and hyperoxygenation have been reported as a pathogenic mechanism inSalmonellaorCitrobacter rodentiuminfection, in patients with HIV and in severe acute malnutrition. We recently found that antioxidants allow strict anaerobes, including methanogenic archaea, to thrive in an oxidative environment (aerobic). Here, we tested the metabolomics switching of the 3 most odorous anaerobic microbes isolated from human gut when grown in aerobiosis with antioxidants.MethodsThree human gut Clostridia,Clostridium sporogenes, Clostridium lituseburenseandClostridium subterminale, isolated by culturomics, were grown in anaerobiosis or in aerobiosis with antioxidants. Gaz and liquid chromatography-Mass spectrometry (GC/MS and LC/MS) were used for metabolomics analysis.ResultsAn unexpected global dichotomic metabolomic switching from thiols, alcohols and short-chain fatty acid esters to a specific aerobic metabolic repertoire with the production of alkanes, cycloheptatriene and, paradoxically, increased butyrate production, was observed. Analysis of polar metabolites confirmed the discovery of an unexplored aerobic metabolic repertoire, including the production of specific dipeptides and several lysophospholipids, thus unraveling unsuspected human gut microbiome capacities.ConclusionsAntioxidants unraveled an unexplored aerobic metabolic repertoire of human gutClostridia. The increased production of butyrate suggests that antioxidants contribute to the maintenance and the active resilience of the human gut microbiome against oxidative aggression, as duringSalmonellainfection.

Wound botulism caused by Clostridium subterminale after a heroin injection

Botulism is caused by toxin production from many species of Clostridium, most commonly Clostridium botulinum as well as C. baratii and C. butyricum. Development of wound botulism is associated with injection drug users but has also been described in traumatic injuries with exposure to soil. A patient presented to the emergency department with a complaint of descending, progressive weakness. He recently reported skin popping with heroin injections. Heptavalent botulinum antitoxin was obtained from the Center for Disease Control and Prevention. On hospital day seven, the anaerobic wound cultures resulted with growth of Clostridium subterminale.

Clostridium subterminale Septicemia in a Patient with Metastatic Gastrointestinal Adenocarcinoma

Clostridium subterminale is a rare member of the Clostridiaceae family that is rarely cultured. This report examines a case of Clostridium subterminale cultured from the blood of a 72-year-old man who was ultimately diagnosed with metastatic gastrointestinal (GI) adenocarcinoma. The patient was receiving treatment for nosocomial pneumonia prior to culture of the C. subterminale, which led to suspicion for malignancy. Extensive GI and oncologic workup demonstrated multiple comorbidities and a primary GI cancer, which likely caused a breach in the GI mucosa and C. subterminale entrance into the bloodstream. After a prolonged intensive care unit (ICU) stay, the patient died on hospital day 23. Though rarely reported, C. subterminale septicemia has been demonstrated in patients with malignancy, specifically of the GI tract. Therefore, this case represents a typical C. subterminale septicemia patient. Given the prevalence of Clostridia and the contemporary emergence of multidrug resistant (MDR) microorganisms, both typical and atypical cases regarding rare members of the species have a significant role in the clinical management and public health planning.

Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia

A Gram-staining-positive, spore-forming, obligately anaerobic, acetogenic bacterium, designated LAM1030T, was isolated from methanogenic consortia enriched from biogas slurry collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM1030T were motile, straight or spiral-rod-shaped. Strain LAM1030T could utilize glucose, fructose, maltose, galactose, lactose, sucrose, cellobiose, mannitol, pyruvate, succinic acid and tryptophan as the sole carbon source. Acetic acid, isovaleric acid and butanoic acid were the main products of glucose fermentation. Sodium sulfite was used as an electron acceptor. Growth of strain LAM1030T was completely inhibited by the addition of ampicillin, tetracycline, gentamicin or erythromycin at a concentration of 20 µg ml−1. The main polar lipids of strain LAM1030T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, 11 unknown glycolipids and two unknown phospholipids. No respiratory quinone was detected. The major fatty acids of strain LAM1030T were C16 : 0 (21.1 %), C14 : 0 (10.3 %), summed feature 9 (including C16:0 10-methyl and/or iso-C17:1 ω9c) (11.3% ), summed feature 3 (including C16:1 ω7c and/or C16:1 ω6c) (10.6% ) and iso-C15 : 0 (6.6 %). Analysis of the 16S rRNA gene sequence indicated that strain LAM1030T belonged to the genus Clostridium and was most closely related to Clostridium subterminale DSM 6970T, Clostridium thiosulfatireducens DSM 13105T and Clostridium sulfidigenes DSM 18982T, with 97.0, 96.9 and 96.8 % similarity, respectively. The G+C content of the genomic DNA of strain LAM1030T was 31.2±0.3 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characterization, strain LAM1030T is suggested to represent a novel species of the genus Clostridium , for which the name Clostridium huakuii sp. nov. is proposed. The type strain is LAM1030T ( = ACCC 00698T = JCM 19186T).