Intestinal gluconeogenesis shapes gut microbiota, fecal and urine metabolome in mice with gastric bypass surgery.

Intestinal gluconeogenesis (IGN), gastric bypass (GBP) and gut microbiota positively regulate glucose homeostasis and diet-induced dysmetabolism. GBP modulates gut microbiota, whether IGN could shape it has not been investigated. We studied gut microbiota and microbiome in wild type and IGN-deficient mice, undergoing GBP or not, and fed on either a normal chow (NC) or a high-fat/high-sucrose (HFHS) diet. We also studied fecal and urine metabolome in NC-fed mice. IGN and GBP had a different effect on the gut microbiota of mice fed with NC and HFHS diet. IGN inactivation increased abundance of Deltaproteobacteria on NC and of Proteobacteria such as Helicobacter on HFHS diet. GBP increased abundance of Firmicutes and Proteobacteria on NC-fed WT mice and of Firmicutes, Bacteroidetes and Proteobacteria on HFHS-fed WT mice. The combined effect of IGN inactivation and GBP increased abundance of Actinobacteria on NC and the abundance of Enterococcaceae and Enterobacteriaceae on HFHS diet. A reduction was observed in the amounf of short-chain fatty acids in fecal (by GBP) and in both fecal and urine (by IGN inactivation) metabolome. IGN and GBP, separately or combined, shape gut microbiota and microbiome on NC- and HFHS-fed mice, and modify fecal and urine metabolome.

Dysbiosis of Gut Microbiota Promotes Hepatocellular Carcinoma Progression by Regulating the Immune Response.

METHOD: This study included 74 Chinese male patients with HCC. They were divided into early (n = 19), intermediate (n = 37), and terminal (n = 18) groups, referred to as Barcelona Clinic Liver Cancer stage 0+A, B, and C+D, respectively. Paired fecal and plasma samples were collected. Microbial composition and profiles were analyzed by 16S rRNA gene sequencing. The levels of gut damage marker (regenerating islet-derived protein 3α (REG3α)) and microbial translocation markers (soluble CD14 (sCD14), lipopolysaccharide-binding protein (LBP), peptidoglycan recognition proteins (PGRPs)) were determined in plasma samples of patients by ELISA. Twenty plasma cytokine and chemokines were determined by Luminex. RESULTS: In early, intermediate, and terminal groups, the abundance of the Bifidobacteriaceae family decreased significantly (3.52%, 1.55%, and 0.56%, respectively, P = 0.003), while the abundance of the Enterococcaceae family increased significantly (1.6%, 2.9%, and 13.4%, respectively, P = 0.022). Levels of REG3α and sCD14 were markedly elevated only in the terminal group compared with the early (P = 0.025 and P = 0.048) and intermediate groups (P = 0.023 and P = 0.046). The level of LBP significantly increased in the intermediate (P = 0.035) and terminal (P = 0.025) groups compared with the early group. The PGRP levels were elevated only in the terminal group compared with the early group (P = 0.018). The ratio of Enterococcaceae to Bifidobacteriaceae was significantly associated with the levels of REG3α, LBP, sCD14, and PGRPs. With HCC progression, increased levels of inflammatory cytokines accompanied by a T cell-immunosuppressive response and microbial translocation were observed. CONCLUSION: Gut microbiota compositional and functional shift, together with elevated gut damage and microbial translocation, may promote HCC development by stimulating inflammatory response and suppressing T cell response.

Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus.

A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17AT and HDW17BT, isolated from the intestine of the diving beetle Cybister lewisianus, and the dark diving beetle Hydrophilus acuminatus, respectively. Both strains were Gram-positive and facultative anaerobic cocci forming cream-colored colonies. The isolates grew optimally at 25°C, pH 7, in the presence of 0.3% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolates were members of the genus Vagococcus, and strain HDW17AT was closely related to Vagococcus fessus CCUG 41755T (98.9% of 16S rRNA gene sequence similarity and 74.3% of average nucleotide identity [ANI]), whereas strain HDW17BT was closely related to Vagococcus fluvialis NCFB 2497T (98.9% of 16S rRNA gene sequence similarity and 76.6% of ANI). Both strains contained C16:0, and C18:1ω9c as the major cellular fatty acids, but C16:1ω9c was also observed only in strain HDW17BT as the major cellular fatty acid. The respiratory quinone of the isolates was MK-7. The major polar lipid components were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The genomic DNA G + C content of strains HDW17AT and HDW17BT were 36.6 and 34.4%, respectively. Both strains had cell wall peptidoglycan composed of the amino acids L-alanine, glycine, D-glutamic acid, L-tryptophan, L-lysine, and L-aspartic acid, and the sugars ribose, glucose, and galactose. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW17AT and HDW17BT represent two novel species in the genus Vagococcus. We propose the name Vagococcus coleopterorum sp. nov. for strain HDW17AT (= KACC 21348T = KCTC 49324T = JCM 33674T) and the name Vagococcus hydrophili sp. nov. for strain HDW17BT (= KACC 21349T = KCTC 49325T = JCM 33675T).

Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content.

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49T, was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai-Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49T was closely related to Vagococcus elongatus CCUG 51432T (96.5 % similarity), Vagococcus fluvialis NCFB 2497T (96.0 %) and Vagococcus lutrae CCUG 39187T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N-acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp). The major cellular fatty acids (>10 %) were C16 : 0 (35.6 %), C14 : 0 (17.3 %), C18 : 1 ω9c (16.2 %) and C16 : 1 ω9c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA-DNA hybridization of strain CF-49T with V. fluvialis DSM 5731T, V. elongatus CCUG 51432Tand V. lutrae CCUG 39187T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus, with the name Vagococcus xieshaowenii. The type strain is CF-49T (=CGMCC 1.6436T=GDMCC 1.1588T=JCM 33477T).

Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound.

Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1 %), followed by SS1994T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcusvulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.

Effect of nutritional interventions with quercetin, oat hulls, ß-glucans, lysozyme and fish oil on performance and health status related parameters of broilers chickens.

1. An experiment was conducted to evaluate the effects of technical feed ingredients between 14 and 28 d of age on performance and health status of broilers (d 14-35) fed diets with a high inclusion rate of rapeseed meal as a nutritional challenge. It was hypothesized that the feed ingredients would improve health status related parameters. 2. A total of 1008 one-day-old male Ross 308 chicks were distributed over 36 floor pens and allocated to one of six iso-caloric (AMEN 13 MJ/kg) growing diets (d 15-28): a control and five test diets supplemented with quercetin (400 mg/kg), oat hulls (50 g/kg), ß-glucan (100 mg/kg), lysozyme (40 mg/kg) or fish oil ω-3 fatty acids (40 g/kg), with six replicate pens per treatment. 3. Dietary inclusion of oat hulls and lysozyme resulted in a reduction in broiler performance during the first week after providing the experimental diets. 4. No effect of interventions on the microbiota diversity in the jejunum and ileum was observed. Ileal microbiota composition of birds fed oat hulls differed from the other groups, as shown by a higher abundance of the genus Enterococcus, mainly at the expense of the genus Lactobacillus. 5. In the jejunum, villus height and crypt depth of lysozyme-fed birds at d 28 were decreased compared to the control group. Higher total surface area of villi occupied by goblet cells and total villi surface area in jejunum (d 21 and 28) were observed in chickens fed oat hulls compared to other groups. 6. Genes related to the growth-factor-activity pathway were more highly expressed in birds fed ß-glucan compared to the control group, while the genes related to anion-transmembrane-transporter-activity pathway in the quercetin- and oat hull-fed birds were less expressed. The genes differently expressed between dietary interventions did not seem to be directly involved in immune related processes. 7. It was concluded that the tested nutritional interventions in the current experiment only marginally effected health status related parameters.

Vagococcus teuberi sp. nov., isolated from the Malian artisanal sour milk fènè.

Ten bacterial isolates belonging to the genus Vagococcus were obtained from Malian sour milk fènè produced from spontaneously fermented cow milk. However, these isolates could not be assigned to a species upon initial comparative 16S rRNA gene sequence analysis and were therefore further characterized. Rep-PCR fingerprinting of the isolates yielded four strain clusters represented by strains CG-21T (=DSM 21459T), 24CA, CM21 and 9H. Sequence identity of the 16S rRNA gene of DSM 21459T to its closest relative species Vagococcus penaei was 97.9%. Among the four rep strain clusters, DSM 21459T and 24CA shared highest 16S rRNA gene sequence identity of 99.6% while CM21 and 9H shared 98.6-98.8% with DSM 21459T and V. penaei CD276T. DSM 21459T and 24CA were thus subjected to a polyphasic typing approach. The genome of DSM 21459T featured a G+C content of 34.1mol% for a 2.17-bp chromosome and a 15-kbp plasmid. Average nucleotide identity (ANI) of DSM 21459T to Vagococcus fluvialis bH819, V. penaei CD276T were 72.88%, 72.63%, respectively. DNA-DNA hybridization (DDH) similarities of strain DSM 21459T to other Vagococcus species were <42.0%. ANI and DDH findings strongly supported the 16S rRNA gene phylogenetic tree delineations. The fatty acid patterns of DSM 21459T was palmitic acid (C 16:0, 24.5%), oleic acid (C 18:1-ω9c, 32.8%), stearic acid (C 18:0, 18.9%). General physiological characterization of DSM 21459T and 24CA were consistent with those of the genus Vagococcus. Strain DSM 21459T and further strains are therefore considered to belong to a novel species, for which the nomenclature Vagococcus teuberi sp. nov. is proposed. The type strain is named CG-21T (=DSM 21459T and LMG 24695T).

Vagococcus humatus sp. nov., isolated from soil beneath a decomposing pig carcass.

A Gram-stain-positive, non-motile, coccus-shaped bacterium, designated strain C25T, was isolated from the soil beneath a decomposing pig carcass in Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain C25T belongs to the genus Vagococcus in the family Enterococcaceae of the Lactobacillales. 16S rRNA gene sequence analysis showed that strain C25T was closely related to Vagococcus lutrae CCUG 39187T (96.5 % similarity) and Enterococcus termitis LMG 8895T (95.8 %). The chemotaxonomic properties of strain C25T were consistent with those of the genus Vagococcus; the major cellular fatty acids consisted of C16 : 0, C16 : 1ω9c and C18 : 1ω9c, and the cell-wall peptidoglycan type was based on meso-diaminopimelic acid. The G+C content of the genomic DNA was 44 mol%. On the basis of phylogenetic inference, fatty acid profile, and chemotaxonomic and other phenotypic properties, strain C25T is clearly differentiated from closely related type strains of the genus Vagococcus and represents a novel species in this genus, for which the name Vagococcus humatus sp. nov. is proposed. The type strain is C25T (=KEMB 562-002T=JCM 31581T).

Isolation and characterization of Vagococcus sp from midgut of Culex quinquefasciatus (Say) mosquito.

BACKGROUND & OBJECTIVES: Mosquito gut is a rich source of microorganisms. These microorganisms exhibit close association and contribute various physiological processes taking place in mosquito gut. The present study is aimed to characterize two bacterial isolates M19 and GB11 recovered from the gut of Culex quinquefasciatus mosquito collected from Bhuj and Jamnagar districts of Gujarat, India. METHODS: Both the strains were characterized using polyphasic approach including, phenotypic characterization, whole cell protein profiling and sequencing of 16S rRNA gene and groESL region. RESULTS: Sequences of 16S rRNA gene of M19 and GB11 were 99% similar to Vagococcus carniphilus and Vagococcus fluvialis. But phenotypic profile, whole cell protein profile and sequence of groESL region of both isolates were found to be similar to V. fluvialis. CONCLUSION: Based on phenotypic, genotypic and protein profiling, both the strains were identified as V. fluvialis. So far this species was known from domestic animals and human sources only. This is the first report of V. fluvialis inhabiting midgut of Cx. quinquefasciatus mosquito collected from Arabian sea coastal of India.

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality.

BACKGROUND: Bacterial translocation from the gut plays an important role in the pathophysiology of acute-on-chronic liver failure (ACLF). However, gut dysbiosis in ACLF was not widely documented in previous studies. AIM: This research characterized the fecal microbiota in patients with ACLF and analyzed the temporal stability of gut microbiota during illness. METHODS: Fecal microbiota of 79 ACLF patients (42 patients were followed in the next 4 weeks after the first visit for longitudinal study) and 50 healthy controls was analyzed by 16S ribosomal DNA pyrosequencing. RESULTS: There was a marked difference between the ACLF group and the control group. The overall microbial diversity and richness were significantly lower in ACLF than in controls. ACLF patients had lower abundance of Bacteroidaceae, Ruminococcaceae, and Lanchnospiraceae, but higher abundance of Pasteurellaceae, Streptococcaceae, and Enterecoccaceae. The relative abundance of Lachnospiraceae was obviously decreased in ACLF patients with hepatic encephalopathy. The gut microbiota kept relatively stable in a short term after the onset of ACLF. The use of antibiotics only showed moderate impacts on the gut microbiota. The relative abundance of Pasteurellaceae and Model of End Stage Liver Disease score were independent factors predicting mortality rate. Network analysis comparison showed robust correlations between specific bacterial families (Ruminococcaceae and Lachnospiraceae) and inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor alpha, IL-2) in ACLF patients. CONCLUSIONS: These data suggest gut dysbiosis in ACLF and its predictive value for mortality. The results thus open up the possibility of designing diagnostic biomarkers and targeted probiotics aimed at decreasing mortality in ACLF.

Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, T. halophilus subsp. halophilus subsp. nov. and T. halophilus subsp. flandriensis subsp. nov.

Most bacteria recovered so far from sugar thick juice during storage represent strains of the species Tetragenococcus halophilus. Recently, several Gram-positive, non-motile, non-spore-forming cocci with other physiological and genetic traits were isolated from sugar thick juice samples from different origins. In this study, representative isolates were investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%. The level of DNA-DNA relatedness between isolate T1(T), representing the newly found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic features demonstrated that the isolates represent a novel species, for which the name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from high-salt and high-sugar environments showed clear differences in several physiological and genetic characteristics like RAPD fingerprints and 16S rRNA gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness between osmophilic and halophilic T. halophilus isolates, demonstrating that the different strains belong to the same species. Based on the phenotypic and genotypic differences observed, as well as the different origins of the strains and the industrial relevance of thick juice degradation, two subspecies of T. halophilus are described in this manuscript: T. halophilus subsp. halophilus subsp. nov. for the strains isolated from salt media and T. halophilus subsp. flandriensis subsp. nov. for the strains isolated from sugar-rich environments, which were first isolated in Flanders, Belgium. The type strains for the subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T) =DSM 23766(T)), respectively.

Relationship between mucosa-associated microbiota and inflammatory parameters in the ileal pouch after restorative proctocolectomy for ulcerative colitis.

BACKGROUND: Our aim was to assess the relationship between the ileal-pouch microbiota and inflammatory parameters in patients operated on for ulcerative colitis. METHODS: In this cross-sectional study, 32 consecutive outpatients returning for follow-up endoscopy were recruited. Pouch biopsies were obtained during endoscopy for culture of bacteria adherent to the mucosa, histology, and analysis of local inflammation (IL-1ß, IL-6, and TNFα by immunometric assay; and toll-like receptor [TLR] 2 and 4 mRNA by quantitative real-time PCR). Fecal samples were collected for analysis of lactoferrin by ELISA. RESULTS: Granulocyte and monocyte mucosal infiltration correlated directly with mucosal Bacteriodiaceae spp. counts. Clostridiaceae spp. counts showed a direct correlation with mucosal ulceration and number of daily stools. In patients with pouchitis, Enterococcaceae spp. counts were less than in healthy patients. Enterobacteriaceae spp., Streptococcaceae spp. and Enterococcaceae spp. counts correlated inversely with immune cell infiltration. TLR-2 and TLR-4 mRNA, and mucosal levels of IL-1ß levels all correlated directly with Veilonella spp. counts. CONCLUSION: Bacteriodaceae spp. and, Clostridiaceae spp. may be associated with inflammation of the pouch mucosa. Conversely, Enterococcaceae spp., and possibly Enterobacteriaceae spp. and Streptococcaceae spp., may have an active role in maintaining immunologic homeostasis within the pouch mucosa.

Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei).

A polyphasic taxonomic study, using phenotypic, phylogenetic and genotypic characterization, was performed on five Gram-stain-positive, catalase-negative, coccus-shaped Vagococcus-like bacteria isolated from the spoilage microbiota of cooked shrimp. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Vagococcus. The five isolates shared 100% 16S rRNA gene sequence similarity, and representative strain CD276(T) formed a branch that was distinct from the type strains of the six recognized species of the genus Vagococcus (Vagococcus fluvialis CCUG 32704(T), V. salmoninarum NCFB 2777(T), V. lutrae CCUG 39187(T), V. fessus M2661/98/1(T), V. carniphilus ATCC BAA-340(T) and V. elongatus PPC9(T)). The taxonomic position of strain CD276(T) was clarified using DNA-DNA hybridization, pulsed-field gel electrophoresis of whole-genome DNA, G+C content determination, cell-wall peptidoglycan typing, fatty acid analysis and biochemical characterization. On the basis of this evidence, a novel species, Vagococcus penaei sp. nov., is proposed. The type strain is CD276(T) (=LMG 24833(T) =CIP 109914(T)).