Mucosal-associated invariant T cells and Vδ2+ γδ T cells in community acquired pneumonia: association of abundance in sputum with clinical severity and outcome.

Mucosal-associated invariant T (MAIT) cells and Vδ2+ γδ T cells are anti-bacterial innate-like lymphocytes (ILLs) that are enriched in blood and mucosa. ILLs have been implicated in control of infection. However, the role of ILLs in community-acquired pneumonia (CAP) is unknown. Using sputum samples from a well-characterized CAP cohort, MAIT cell and Vδ2+ T cell abundance was determined by quantitative polymerase chain reaction (qPCR). Cytokine and chemokine concentrations in sputum were measured. The capacity of bacteria in sputum to produce activating ligands for MAIT cells and Vδ2+ T cells was inferred by 16S rRNA sequencing. MAIT cell abundance in sputum was higher in patients with less severe pneumonia; duration of hospital admission was inversely correlated with both MAIT and Vδ2+ T cell abundance. The abundance of both ILLs was higher in patients with a confirmed bacterial aetiology; however, there was no correlation with total bacterial load or the predicted capacity of bacteria to produce activating ligands. Sputum MAIT cell abundance was associated with interferon (IFN)-α, IFN-γ, and sputum neutrophil abundance, while Vδ2+ T cell abundance was associated with CXCL11 and IFN-γ. Therefore, MAIT and Vδ2+ T cells can be detected in sputum in CAP, where they may contribute to improved clinical outcome.

Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils.

An aerobic, thermophilic, moderately acidophilic non-spore-forming bacterium, strain K22(T), was isolated from geothermally heated soil at Mount Ngauruhoe, New Zealand. On the basis of 16S rRNA gene sequence similarity, K22(T) was shown to belong to subdivision 4 of the phylum Acidobacteria and to be most closely related to 'Candidatus Chloracidobacterium thermophilum' (86 %) and Blastocatella fastidiosa (86 %). Cells stained Gram-negative and were catalase and oxidase-positive. The major fatty acids detected were iso-C15 : 0, iso-C17 : 0, iso-C19 : 0 and iso-C21 : 0 when standard lipid extraction protocols were employed. Analysis of the total cell lipid acid hydrolysate also detected membrane-spanning and ether lipids, which made up approximately 40 % of the total membrane composition. These lipids included dicarboxylic (iso-diabolic) acid and the glyceryl ether of alkyl analogues of iso-C15 : 0 and iso-diabolic acid. The G+C content of the genomic DNA was 59.6 mol% and the primary respiratory quinone was MK-8. Strain K22(T) grew at 50-69 °C with an optimum temperature of 65 °C and at pH 4.1-7.8 with an optimum growth pH of 6.5. NaCl tolerance was up to 1 % (w/v). Cells displayed a chemoheterotrophic and obligately aerobic metabolism. Cells grew on nutrient broth, alginate, arabinose, Casamino acids, glucose, lactate, formate, mannose, sodium alginate, peptone, sucrose, tryptone, xanthan, xylan, xylose and yeast extract. Nitrogen sources included nitrate, ammonium, urea, yeast extract and Casamino acids, but not dinitrogen gas. The distinct phylogenetic position and the phenotypic characteristics separate strain K22(T) from all other members of the class Acidobacteria and indicate that it represents a novel species and genus, for which the name Pyrinomonas methylaliphatogenes gen. nov., sp. nov. is proposed. The type strain of the type species is K22(T) ( = DSM 25857(T) = ICMP 18710(T)).

Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions.

Small-subunit (SSU) rRNA gene sequences associated with the phylum Armatimonadetes were analyzed using multiple phylogenetic methods, clarifying both the phylum boundary and the affiliation of previously ambiguous groupings. Here we define the Armatimonadetes as 10 class-level groups and reclassify two previously associated groups as candidate divisions WS1 and FBP.

Dientamoeba fragilis associated with microbiome diversity changes in acute gastroenteritis patients.

This study examined the correlation between intestinal protozoans and the bacterial microbiome in faecal samples collected from 463 patients in New Zealand who were diagnosed with gastroenteritis. In comparison to traditional microscopic diagnosis methods, Multiplexed-tandem PCR proved to be more effective in detecting intestinal parasites. Among the identified protozoans, Blastocystis sp. and Dientamoeba fragilis were the most prevalent. Notably, D. fragilis was significantly associated with an increase in the alpha-diversity of host prokaryotic microbes. Although the exact role of Blastocystis sp. and D. fragilis as the primary cause of gastroenteritis remains debatable, our data indicates a substantial correlation between these protozoans and the prokaryote microbiome of their hosts, particularly when compared to other protists or patients with gastroenteritis but no detectable parasitic cause. These findings underscore the significance of comprehending the contributions of intestinal protozoans, specifically D. fragilis, to the development of gastroenteritis and their potential implications for disease management.

Complete Genome Sequences of Kinneretia sp. Strain XES5, Shinella sp. Strain XGS7, and Vogesella sp. Strain XCS3, Isolated from Xenopus laevis Skin.

Here, we report the genome sequences of three bacterial isolates, Kinneretia sp. strain XES5, Shinella sp. strain XGS7, and Vogesella sp. strain XCS3, which were cultured from skin of adult female laboratory-bred Xenopus laevis.

Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.

Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×109 cfu), or B. animalis subsp. lactis HN019 (9×109 cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.

Fatty Acids of Chthonomonas calidirosea, of a novel class Chthonomonadetes from a recently described phylum Armatimonadetes.

A Gram-negative, aerobic, pink-pigmented, rod-shaped bacterium Chthonomonas calidirosea (strain T49(T)) with an optimal temperature for growth of 68 °C, isolated from soil samples from Hell's Gate in the Tikitere geothermal system (New Zealand), was the first cultivated bacterium of the novel phylum Armatimonadetes (formerly candidate division OP10). The lipid composition of C. calidirosea presents a number of unusual features both in the fatty acids and polar lipids. This contribution reports on the fatty acid profile of C. calidirosea. Transmethylation of bacterial biomass yielded fatty acid methyl esters and hydrocarbons, including squalene, partially hydrogenated squalenes, and diploptene. The only type of unsaturation found in C. calidirosea fatty acids was cis-Δ5, as revealed by GCMS of dimethyl disulfide (DMDS) adducts, and the lack of trans-unsaturation absorbance at 960-980 cm(-1) in the IR spectrum of fatty acids methyl esters. An unidentified component X with ECL 16.86 (BP1) and ECL 17.27 (BP20) was also observed, with molecular ion at m/z 282 ("17:1"). X did not form DMDS adducts, nor was affected by mild hydrogenation conditions, indicating the likely presence of a ring rather than unsaturation. The presence of a cyclopropane ring with cis-stereochemistry was confirmed by the (1)H-NMR spectrum. Hydrogenation of X in acetic acid resulted in formation of straight chain 17:0, 5-methyl- and 6-methyl-16:0 fatty acid methyl esters, thus confirming the structure of a novel 5,6-methylene hexadecanoic acid. The major fatty acids of a solid media-grown C. calidirosea were as follows (in weight % of total fatty acids): 16:0 (25.8), i17:0 (19.3), ai17:0 (13.5), 16:1∆5 (8.8), i17:1∆5 (6.8), 5,6-methylene 16:0 (5.2), i16:0 (4.4), 18:0 (3.6), 18:1∆5 (3.2).