Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model.

Bacterial vaginosis (BV) is a gynecologic disorder characterized by a shift in cervicovaginal microbiota from Lactobacillus spp. dominance to a polymicrobial biofilm composed of diverse anaerobes. We utilized a well-characterized human three-dimensional cervical epithelial cell model in conjunction with untargeted metabolomics and immunoproteomics analyses to determine the immunometabolic contribution of three members of the Veillonellaceae family: Veillonella atypica, Veillonella montpellierensis and Megasphaera micronuciformis at this site. We found that Veillonella spp. infections induced significant elevation of polyamines. M. micronuciformis infections significantly increased soluble inflammatory mediators, induced moderate levels of cell cytotoxicity, and accumulation of cell membrane lipids relative to Veillonella spp. Notably, both V. atypica and V. montpellierensis infections resulted in consumption of lactate, a key metabolite linked to gynecologic and reproductive health. Collectively our approach and data provide unique insights into the specific contributions of Veillonellaceae members to the pathogenesis of BV and women's health.

Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron.

A large variety of microbes are present in the human gut, some of which are considered to interact with each other. Most of these interactions involve bacterial metabolites. Phascolarctobacterium faecium hardly uses carbohydrates for growth and instead uses succinate as a substrate. This study investigated the growth behavior of the co-culture of the succinate-specific utilizer P. faecium and the succinogenic gut commensal Bacteroides thetaiotaomicron. Succinate production by B. thetaiotaomicron supported the growth of P. faecium and concomitant propionate production via the succinate pathway. The succinate produced was completely converted to propionate. This result was comparable with the monoculture of P. faecium in the medium supplemented with 1% (w/v) succinate. We analyzed the transcriptional response (RNA-Seq) between the mono- and co-culture of P. faecium and B. thetaiotaomicron. Comparison of the expression levels of genes of P. faecium between the mono- and co-cultured conditions highlighted that the genes putatively involved in the transportation of succinate were notably expressed under the co-cultured conditions. Differential expression analysis showed that the presence of P. faecium induced changes in the B. thetaiotaomicron transcriptional pattern, for example, expression changes in the genes for vitamin B12 transporters and reduced expression of glutamate-dependent acid resistance system-related genes. Also, transcriptome analysis of P. faecium suggested that glutamate and succinate might be used as sources of succinyl-CoA, an intermediate in the succinate pathway. This study revealed some survival strategies of asaccharolytic bacteria, such as Phascolarctobacterium spp., in the human gut.

Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient.

Strain Marseille-P2082, an anaerobic, non-motile, asporogenous, Gram-negative, coccoid bacterium was isolated from the faeces of a 33 year-old obese French woman before bariatric surgery. The isolate exhibits 98.65% 16S rRNA gene nucleotide sequence similarity with Negativicoccus succinicivorans strain ADV 07/08/06-B-1388T, its current closest phylogenetic neighbour with standing in nomenclature. However, the dDDH relatedness between the new isolate and N. succinicivorans type strain ADV 07/08/06-B-1388T is 52.5 ± 2.7%. Strain Marseille-P2082 has a genome of 1,360,589 bp with a 51.1% G+C content. Its major fatty acids were identified as C18:1n9, C18:0 and C16:0. Based on its phenotypic, genomic and phylogenetic characteristics, strain Marseille-P2082T [= CSURP2082 (Collection de Souches de l'Unité des Rickettsies) = DSM 100853] is proposed as the type strain of the novel species Negativicoccus massiliensis sp. nov. The 16S rRNA gene sequence and whole-genome shotgun sequence have been deposited in EMBL-EBI under accession numbers LN876651 and LT700188, respectively.

Host-microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake.

Aberrant microbiota composition and function have been linked to several pathologies, including type 2 diabetes. In animal models, prebiotics induce favourable changes in the intestinal microbiota, intestinal permeability (IP) and endotoxaemia, which are linked to concurrent improvement in glucose tolerance. This is the first study to investigate the link between IP, glucose tolerance and intestinal bacteria in human type 2 diabetes. In all, twenty-nine men with well-controlled type 2 diabetes were randomised to a prebiotic (galacto-oligosaccharide mixture) or placebo (maltodextrin) supplement (5·5 g/d for 12 weeks). Intestinal microbial community structure, IP, endotoxaemia, inflammatory markers and glucose tolerance were assessed at baseline and post intervention. IP was estimated by the urinary recovery of oral 51Cr-EDTA and glucose tolerance by insulin-modified intravenous glucose tolerance test. Intestinal microbial community analysis was performed by high-throughput next-generation sequencing of 16S rRNA amplicons and quantitative PCR. Prebiotic fibre supplementation had no significant effects on clinical outcomes or bacterial abundances compared with placebo; however, changes in the bacterial family Veillonellaceae correlated inversely with changes in glucose response and IL-6 levels (r -0·90, P=0·042 for both) following prebiotic intake. The absence of significant changes to the microbial community structure at a prebiotic dosage/length of supplementation shown to be effective in healthy individuals is an important finding. We propose that concurrent metformin treatment and the high heterogeneity of human type 2 diabetes may have played a significant role. The current study does not provide evidence for the role of prebiotics in the treatment of type 2 diabetes.

Improved cathode for high efficient microbial-catalyzed reduction in microbial electrosynthesis cells.

Microbial electrosynthesis cells (MECs) are devices wherein microorganisms can electrochemically interact with electrodes, directly donating or accepting electrons from electrode surfaces. Here, we developed a novel cathode by using nickel nanowires anchored to graphite for the improvement of microbial-catalyzed reduction in MEC cathode chamber. This porous nickel-nanowire-network-coated graphite electrode increased the interfacial area and interfacial interactions between the cathode surface and the microbial biofilm. A 2.3 fold increase in bio-reduction rate over the untreated graphite was observed. Around 282 mM day(-1) m(-2) of acetate resulting from the bio-reduction of carbon dioxide by Sporomusa was produced with 82 ± 14% of the electrons consumed being recovered in acetate.

Modulation of the fecal bile acid profile by gut microbiota in cirrhosis.

BACKGROUND & AIMS: The 7α-dehydroxylation of primary bile acids (BAs), chenodeoxycholic (CDCA) and cholic acid (CA) into the secondary BAs, lithocholic (LCA) and deoxycholic acid (DCA), is a key function of the gut microbiota. We aimed at studying the linkage between fecal BAs and gut microbiota in cirrhosis since this could help understand cirrhosis progression. METHODS: Fecal microbiota were analyzed by culture-independent multitagged-pyrosequencing, fecal BAs using HPLC and serum BAs using LC-MS in controls, early (Child A) and advanced cirrhotics (Child B/C). A subgroup of early cirrhotics underwent BA and microbiota analysis before/after eight weeks of rifaximin. RESULTS: Cross-sectional: 47 cirrhotics (24 advanced) and 14 controls were included. In feces, advanced cirrhotics had the lowest total, secondary, secondary/primary BA ratios, and the highest primary BAs compared to early cirrhotics and controls. Secondary fecal BAs were detectable in all controls but in a significantly lower proportion of cirrhotics (p<0.002). Serum primary BAs were higher in advanced cirrhotics compared to the rest. Cirrhotics, compared to controls, had a higher Enterobacteriaceae (potentially pathogenic) but lower Lachonospiraceae, Ruminococcaceae and Blautia (7α-dehydroxylating bacteria) abundance. CDCA was positively correlated with Enterobacteriaceae (r=0.57, p<0.008) while Ruminococcaceae were positively correlated with DCA (r=0.4, p<0.05). A positive correlation between Ruminococcaceae and DCA/CA (r=0.82, p<0.012) and Blautia with LCA/CDCA (r=0.61, p<0.03) was also seen. Prospective study: post-rifaximin, six early cirrhotics had reduction in Veillonellaceae and in secondary/primary BA ratios. CONCLUSIONS: Cirrhosis, especially advanced disease, is associated with a decreased conversion of primary to secondary fecal BAs, which is linked to abundance of key gut microbiome taxa.

Mitsuokella jalaludinii inhibits growth of Salmonella enterica serovar Typhimurium.

Salmonella continues to be a significant human health threat, and the objective of this study was to identify microorganisms with the potential to improve porcine food-safety through their antagonism of Salmonella. Anaerobic culture supernatants of 973 bacterial isolates from the gastrointestinal tract and feces of swine were screened for their capacity to inhibit the growth of Salmonella enterica serovar Typhimurium. Growth inhibition of 1000-fold or greater was observed from 16 isolates, and 16S rRNA sequencing identified the isolates as members of the genera Mitsuokella, Escherichia/Shigella, Anaerovibrio, Selenomonas, and Streptococcus. Four isolates were identified as Mitsuokella jalaludinii, and the mechanism of Salmonella Typhimurium growth inhibition by M. jalaludinii was further investigated. M. jalaludinii stationary phase culture supernatants were observed to significantly inhibit growth, and featured the production of lactic, succinic, and acetic acids. Aerobic and anaerobic S. Typhimurium growth was restored when the pH of the culture supernatants (pH 4.6) was increased to pH 6.8. However, S. Typhimurium growth in fermentation acid-free media was the same at pH 4.6 and pH 6.8 - indicating a synergistic effect between fermentation acid production and low pH as the cause of S. Typhimurium growth inhibition. Furthermore, exposure of S. Typhimurium to M. jalaludinii culture supernatants inhibited Salmonella invasion of HEp-2 cells by 10-fold. The results identify M. jalaludinii as a possible inhibitor of Salmonella growth and invasion in swine, and thus a potential probiotic capable of improving food safety.

Effects of freeze-dried Mitsuokella jalaludinii culture and Natuphos(®) phytase supplementation on the performance and nutrient utilisation of broiler chickens.

BACKGROUND: Phytate-bound phosphorus (P) in poultry diets is poorly available to chickens. Hence exogenous phytase is often added to their diets. Mitsuokella jalaludinii is a rumen bacterial species that produces high phytase activity. In this study the effects of freeze-dried active M. jalaludinii culture (FD-AMJC) and Natuphos(®) phytase (phytase N) supplementations on the growth performance and nutrient utilisation of broiler chickens fed a low-available P (aP) diet were evaluated. RESULTS: Supplementation of FD-AMJC or phytase N to the low-aP diet improved the feed intake, feed conversion rate, body weight gain, dry matter (DM) digestibility and P, Ca and Mn retention, increased the tibia bone ash content, Ca and P concentrations in tibia DM and P and Zn concentrations in plasma and reduced the P excretion of broiler chickens. However, the feed conversion rate, P and Ca retention, DM digestibility and reduction of P excretion were better with FD-AMJC than phytase N supplementation. Supplementation of FD-AMJC to the low-aP diet also improved the apparent metabolisable energy value of the diet, Cu and Zn retention and crude protein digestibility, but phytase N supplementation did not. CONCLUSION: FD-AMJC supplementation was more efficient in improving nutrient utilisation and reducing P excretion in chickens than phytase N supplementation.

Antibiotic manipulation of intestinal microbiota to identify microbes associated with Campylobacter jejuni exclusion in poultry.

The ability of various subsets of poultry intestinal microbiota to protect turkeys from colonization by Campylobacter jejuni was investigated. Community subsets were generated in vivo by inoculation of day-old poults with the cecal contents of a Campylobacter-free adult turkey, followed by treatment with one antimicrobial, either virginiamycin, enrofloxacin, neomycin, or vancomycin. The C. jejuni loads of the enrofloxacin-, neomycin-, and vancomycin-derived communities were decreased by 1 log, 2 logs, and 4 logs, respectively. Examination of the constituents of the derived communities via the array-based method oligonucleotide fingerprinting of rRNA genes detected a subtype of Megamonas hypermegale specific to the C. jejuni-suppressive treatments.

(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces.

Two anaerobic, non-spore-forming, bacteria (YIT 11850(T) and YIT 11860(T)) that stained Gram-negative, were isolated from human faeces. Cells of strain YIT 11850(T) were coccobacilli, asaccharolytic and largely unreactive, with only traces of lactate and propionate as metabolic end products; however, strain YIT 11850(T) was able to decarboxylate succinate to propionate. The DNA G+C content of strain YIT 11850(T) was 51.9 mol%. Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to Dialister propionicifaciens, with 95.1 % sequence similarity between the two taxa. Biochemical data supported the affiliation of strain YIT 11850(T) to the genus Dialister. Strain YIT 11850(T) therefore represents a novel species for which the name Dialister succinatiphilus sp. nov. is proposed; the type strain is YIT 11850(T) (=DSM 21274(T)=JCM 15077(T)). Cells of the other isolate, strain YIT 11860(T), were non-motile, rod-shaped, positive for aesculin hydrolysis, negative for indole production, produced succinic and acetic acids as end products of glucose metabolism and possessed a DNA G+C content of 45.5 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family 'Porphyromonadaceae' related to Barnesiella viscericola (96.0 %); similarity values with species within the family 'Porphyromonadaceae' with validly published names were less than 86 %. Biochemical data supported the affiliation of strain YIT 11860(T) to the genus Barnesiella. Strain YIT 11860(T) therefore represents a novel species for which the name Barnesiella intestinihominis sp. nov. is proposed; the type strain is YIT 11860(T) (=DSM 21032(T)=JCM 15079(T)).

Megamonas rupellensis sp. nov., an anaerobe isolated from the caecum of a duck.

We report here the identification, characterization and culture of a Gram-negative to Gram-variable, rod-shaped, non-spore-forming anaerobic bacterium (strain FM1025(T)) isolated from the caecum of a duck. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that this strain clustered with species of the family 'Acidaminococcaceae', with 94.9 % similarity to Megamonas hypermegale DSM 1672(T) and less than 91 % similarity with type strains of Pectinatus species. Sequence similarities of at least 98-99 % were observed with numerous sequences deposited in GenBank of uncultured strains from human and chicken caecal contents, but this strain is the first isolate of this taxon to be cultivated and described. On the basis of morphological, physiological and phylogenetic features, this strain should be assigned to a novel species in the genus Megamonas, for which the name Megamonas rupellensis sp. nov. is proposed. The type strain is strain FM1025(T) (=DSM 19944(T) =CIP 109788(T)).

Detection of Dialister pneumosintes in the subgingival biofilm of subjects with periodontal disease.

Dialister pneumosintes has been indicated as a potentially new periodontopathic species. This study evaluated the prevalence of this microorganism in saliva and subgingival biofilm from subjects with different periodontal conditions. Subgingival biofilm and saliva samples from 48 subjects with periodontal health (PH) and 116 patients with chronic periodontitis (CP) were obtained. DNA was extracted from the samples and the presence of D. pneumosintes was determined by PCR. Differences in clinical parameters and frequency of D. pneumosintes between groups were sought by Mann-Whitney, Chi-square and Fisher's exact tests. Overall, D. pneumosintes was detected in 47.8% of the biofilm samples, but only in 3% of saliva samples. CP patients presented a significantly greater mean prevalence of this species in sites with periodontal health and periodontal infection (43.5+/-7.4% and 62.1+/-6.4%, respectively) than PH subjects (29.4+/-7.9%) (Mann-Whitney; p<0.01). Moreover, significant associations between the prevalence of D. pneumosintes and pocket depth (p=0.001), attachment loss (p=0.001) and bleeding on probing (GLM, p=0.014) were observed after adjusting for age and gender. These findings corroborate the association of D. pneumosintes with periodontitis.

Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park.

A new anaerobic, thermophilic, facultatively carboxydotrophic bacterium, strain Nor1(T), was isolated from a hot spring at Norris Basin, Yellowstone National Park. Cells of strain Nor1(T) were curved motile rods with a length of 2.6-3 microm, a width of about 0.5 microm and lateral flagellation. The cell wall structure was of the Gram-negative type. Strain Nor1(T) was thermophilic (temperature range for growth was 40-68 degrees C, with an optimum at 60 degrees C) and neutrophilic (pH range for growth was 6.5-7.6, with an optimum at 6.8-7.0). It grew chemolithotrophically on CO (generation time, 1.15 h), producing equimolar quantities of H(2) and CO(2) according to the equation CO+H(2)O-->CO(2)+H(2). During growth on CO in the presence of ferric citrate or amorphous ferric iron oxide, strain Nor1(T) reduced ferric iron but produced H(2) and CO(2) at a ratio close to 1 : 1, and growth stimulation was slight. Growth on CO in the presence of sodium selenite was accompanied by precipitation of elemental selenium. Elemental sulfur, thiosulfate, sulfate and nitrate did not stimulate growth of strain Nor1(T) on CO and none of these chemicals was reduced. Strain Nor1(T) was able to grow on glucose, sucrose, lactose, arabinose, maltose, fructose, xylose and pyruvate, but not on cellobiose, galactose, peptone, yeast extract, lactate, acetate, formate, ethanol, methanol or sodium citrate. During glucose fermentation, acetate, H(2) and CO(2) were produced. Thiosulfate was found to enhance the growth rate and cell yield of strain Nor1(T) when it was grown on glucose, sucrose or lactose; in this case, acetate, H(2)S and CO(2) were produced. In the presence of thiosulfate or ferric iron, strain Nor1(T) was also able to grow on yeast extract. Lactate, acetate, formate and H(2) were not utilized either in the absence or in the presence of ferric iron, thiosulfate, sulfate, sulfite, elemental sulfur or nitrate. Growth was completely inhibited by penicillin, ampicillin, streptomycin, kanamycin and neomycin. The DNA G+C content of the strain was 51.7+/-1 mol%. Analysis of the 16S rRNA gene sequence revealed that strain Nor1(T) belongs to the Bacillus-Clostridium phylum of the Gram-positive bacteria. On the basis of the studied phenotypic and phylogenetic features, we propose that strain Nor1(T) be assigned to a new genus, Thermosinus gen. nov. The type species is Thermosinus carboxydivorans sp. nov. (type strain, Nor1(T)=DSM 14886(T)=VKM B-2281(T)).

Desulfosporomusa polytropa gen. nov., sp. nov., a novel sulfate-reducing bacterium from sediments of an oligotrophic lake.

Five strains of sulfate-reducing bacteria were isolated from the highest positive dilutions of a most probable number (MPN) series supplemented with lactate and inoculated with sediments from the oligotrophic Lake Stechlin. The isolates were endospore-forming and were motile by means of laterally inserted flagella. They stained Gram-negative and contained b-type cytochromes. CO difference spectra indicated the presence of P582 as a sulfite reductase. Phylogenetic analyses of the 16S rDNA sequences revealed that the isolates were very closely affiliated with the genus Sporomusa. However, sulfate and amorphous Fe(OH)(3), but not sulfite, elemental sulfur, MnO(2), or nitrate were used as terminal electron acceptors. Homoacetogenic growth was found with H(2)/CO(2) gas mixture, formate, methanol, ethanol, and methoxylated aromatic compounds. The strains grew autotrophically with H(2) plus CO(2) in the presence or absence of sulfate. Formate, butyrate, several alcohols, organic acids, carbohydrates, some amino acids, choline, and betaine were also utilized as substrates. The growth yield with lactate and sulfate as substrate was 7.0 g dry mass/mol lactate and thus two times higher than in sulfate-free fermenting cultures. All isolates were able to grow in a temperature range of 4-37 degrees C. Physiologically and by the presence of a Gram-negative cell wall, the new isolates resemble known Desulfosporosinus species. However, phylogenetically they are affiliated with the Gram-negative genus Sporomusa belonging to the Selenomonas subgroup of the Firmicutes. Therefore, the new isolates reveal a new phylogenetic lineage of sulfate-reducing bacteria. A new genus and species, Desulfosporomusa polytropa gen. nov., sp. nov. is proposed.

Preventing in vitro lactate accumulation in ruminal fermentations by inoculation with Megasphaera elsdenii.

In vitro fermentations containing a mixed culture of ruminal bacteria (ruminal fluid from a hay-fed steer), buffer, and primarily rapidly degradable substrates (starch, glucose, cellulose, cellobiose, and trypticase) were inoculated with an overnight culture of Megasphaera elsdenii B159. Triplicate flasks were either uninoculated or inoculated to obtain a final concentration of 8.7 x 10(5) and 8.7 x 10(6) colony forming units of M. elsdenii per milliliter of culture fluid. Inoculation with M. elsdenii prevented an accumulation of lactic acid and excessive drop in pH. Lactate peaked at more than 40 mM in untreated cultures. In cultures inoculated with a low dose of M. elsdenii, lactate concentration peaked at approximately 25 mM at 5 h of fermentation but decreased rapidly to less than 5 mM by 7 h of fermentation. With the addition of the high dose of M. elsdenii, lactate was never greater than 2 mM (P < .05) throughout fermentation. Cultures treated with M. elsdenii had greater amounts (P < .05) of isobutyrate, butyrate, isovalerate, and valerate than untreated cultures. After 24 h of fermentation, one-half of the culture fluid was transferred to an equal volume of fresh buffer with substrate but was not inoculated with further quantities of M. elsdenii. Six hours after transfer, cultures that had been originally treated with M. elsdenii had lower (P < .05) amounts of lactate than untreated cultures. Inoculation with M. elsdenii has potential to prevent lactate accumulation in diets containing readily fermentable carbohydrates.