Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson's disease.

Mitochondrial dysfunction plays an important role in Parkinson's disease (PD), with mitochondrial DNA copy number (mtDNA-CN) emerging as a potential marker for mitochondrial health. We investigated the links between blood mtDNA-CN and PD severity and risk using the Accelerating Medicines Partnership program for Parkinson's Disease dataset, replicating our results in the UK Biobank. Our findings reveal that reduced blood mtDNA-CN levels are associated with heightened PD risk and increased severity of motor symptoms and olfactory dysfunction.

PhageGE: an interactive web platform for exploratory analysis and visualization of bacteriophage genomes.

Background: Antimicrobial resistance is a serious threat to global health. Due to the stagnant antibiotic discovery pipeline, bacteriophages (phages) have been proposed as an alternative therapy for the treatment of infections caused by multidrug-resistant pathogens. Genomic features play an important role in phage pharmacology.

Haemoglobin thresholds to define anaemia from age 6 months to 65 years: estimates from international data sources.

Background: Detection of anaemia is crucial for clinical medicine and public health. Current WHO anaemia definitions are based on statistical thresholds (fifth centiles) set more than 50 years ago. We sought to establish evidence for the statistical haemoglobin thresholds for anaemia that can be applied globally and inform WHO and clinical guidelines.

Statistical haemoglobin thresholds to define anaemia across the lifecycle.

Detection of anaemia is critical for clinical medicine and public health. Current WHO values that define anaemia are statistical thresholds (5 centile) set over 50 years ago, and are presently <110g/L in children 6-59 months, <115g/L in children 5-11 years, <110g/L in pregnant women, <120g/L in children 12-14 years of age, <120g/L in non-pregnant women, and <130g/L in men. Haemoglobin is sensitive to iron and other nutrient deficiencies, medical illness and inflammation, and is impacted by genetic conditions; thus, careful exclusion of these conditions is crucial to obtain a healthy reference population.

AmpSeqR: an R package for amplicon deep sequencing data analysis.

Amplicon sequencing (AmpSeq) is a methodology that targets specific genomic regions of interest for polymerase chain reaction (PCR) amplification so that they can be sequenced to a high depth of coverage. Amplicons are typically chosen to be highly polymorphic, usually with several highly informative, high frequency single nucleotide polymorphisms (SNPs) segregating in an amplicon of 100-200 base pair (bp). This allows high sensitivity detection and quantification of the frequency of each sequence within each sample making it suitable for applications such as low frequency somatic mosaicism detection or minor clone detection in mixed samples.

Genomic Analysis and Characterization of sp. nov., a Novel Aerobic Anoxygenic Phototrophic Bacterium, Isolated from Sayram Lake Water.

Aerobic anoxygenic photosynthetic bacteria (AAPB) are a kind of heterotrophic prokaryote that can use bacteriochlorophyll (BChl) for photosynthesis without oxygen production and they are widely distributed in aquatic environments, including oceans, lakes, and rivers. A novel aerobic anoxygenic photosynthetic bacterium strain XJSP was isolated during a study of water microbial diversity in Sayram Lake, Xinjiang Province, China. Strain XJSP was found to grow optimally at 33 °C, pH 7.

Digestive Tract Morphology and Gut Microbiota Jointly Determine an Efficient Digestive Strategy in Subterranean Rodents: Plateau Zokor.

Rodents' lifestyles vary in different environments, and to adapt to various lifestyles specific digestion strategies have been developed. Among these strategies, the morphology of the digestive tracts and the gut microbiota are considered to play the most important roles in such adaptations. However, how subterranean rodents adapt to extreme environments through regulating gut microbial diversity and morphology of the digestive tract has yet to be fully studied.

Polymyxin dose tunes the evolutionary dynamics of resistance in multidrug-resistant Acinetobacter baumannii.

Objectives: Evolutionary principles have informed the design of strategies that slow or prevent antibiotic resistance. However, how antibiotic treatment regimens shape the evolutionary dynamics of resistance mutations remains an open question. Here, we investigate varying concentrations of the last-resort polymyxins on the evolution of resistance in Acinetobacter baumannii.

Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species.

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples.

Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant in a Murine Bloodstream Infection Model.

Multidrug-resistant (MDR) is a critical threat to human health globally. We constructed a genome-scale metabolic model AB5075 for the hypervirulent, MDR strain AB5075. Predictions of nutrient utilization and gene essentiality were validated using Biolog assay and a transposon mutant library.

Halioglobus sediminis sp. nov., isolated from coastal sediment.

A novel aerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain U0301, was isolated from a marine sediment sample in Weihai, China. This strain grew optimally at 33 °C, pH 7.5 and in the presence of 2.

Alteromonas sediminis sp. nov., isolated from sediment in a sea cucumber culture pond.

A novel strain, U0105, was isolated from marine sediment of the coast of Weihai, China. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, rod-shaped and motile. Growth was observed at salinities of 1.

Alteromonas flava sp. nov. and Alteromonas facilis sp. nov., two novel copper tolerating bacteria isolated from a sea cucumber culture pond in China.

Two bacterial strains, P0211 and P0213, were isolated from a sea cucumber culture pond in China. The strains were able to resist high copper levels. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level.

Aliidiomarina celeris sp. nov., isolated from coastal sediment.

A Gram-stain-negative, heterotrophic, facultative anaerobic, gliding and motile bacterium, approximately 0.6-0.9 µm wide and 1.

Agaribacter flavus sp. nov., isolated from red algae.

A Gram-stain-negative, non-motile, aerobic, curved-rod bacterium, designated as strain 2p52, was isolated from the marine algae Gracilaria blodgettii collected off the coast of Lingshui county, in Hainan province, China. Strain 2p52 grew at 15-42 °C (optimally at 30-33 °C), at pH 6.0-10.

Winogradskyella tangerina sp. nov., a member of the Flavobacteriaceae isolated from coastal sediment.

A Gram-stain-negative, rod-shaped bacterium (designated strain M1309), with slow gliding motility, was isolated from marine sediment obtained off the coast of Weihai, PR China. The growth of M1309 was observed at 16-42 °C (optimum, 37 °C) and pH 6.5-8.

Polaribacter tangerinus sp. nov., isolated from sediment in a sea cucumber culture pond.

A Gram-stain-negative, aerobic, non-motile, coccoid, ovoid or rod-shaped, and orange-pigmented bacterial strain, designated WS2-14, was isolated from sediment collected from a sea cucumber culture pond located in Rongcheng, Shandong province, PR China (122° 14' E, 36° 54' N). Strain WS2-14 grew optimally at 28 °C and pH 7.0-7.

Seonamhaeicola marinus sp. nov., isolated from marine algae.

A Gram-stain-negative, facultatively anaerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain B011, was isolated from marine algae Gracilaria blodgettii collected from the coast of Lingshui county, Hainan, China. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B011, Seonamhaeicola algicola (96.8 % 16S rRNA gene sequence similarity) and Seonamhaeicola aphaedonensis (95.

Marinobacter salexigens sp. nov., isolated from marine sediment.

A novel bacterium, designated as strain HJR7, was isolated from a marine sediment sample collected from the coastal area of Weihai, China (121° 57' E, 37° 29' N). Cells were Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped. The temperature, pH and NaCl ranges for growth were determined as 4-40 °C, pH 6.

Confluentibacter citreus sp. nov., isolated from lake sediment, and emended description of the genus Confluentibacter.

A Gram-stain-negative, non-gliding, aerobic and rod-shaped bacterium, designated XJNY, was isolated from Sayram Lake (44° 30' 30.41″ N 81° 12' 39.55″ E), Xinjiang Province, north-west China, and was characterized taxonomically by a polyphasic study.

Crocinitomix algicola sp. nov., isolated from Gracilaria blodgettii.

A Gram-stain-negative, strictly aerobic, non-flagellated, yellow-pigmented, rod-shaped bacterial strain, designated 0182, was isolated from Gracilaria blodgettii, an algae of phylum Rhodophyta collected from coast of Lingshui county, Hainan, China (110° 03' 44.2'' E, 18° 24' 29.8'' N).

Brumimicrobium aurantiacum sp. nov., isolated from coastal sediment.

A Gram-negative, facultatively anaerobic, non-motile, rod-shaped and orange-coloured bacterium, designated N62T, was isolated from marine sediment of the coast of Weihai, PR China. Strain N62T was found to grow optimally at 28-30 °C, pH 7.0-7.

Algoriphagus marinus sp. nov., isolated from marine sediment and emended description of the genus Algoriphagus.

A Gram-stain-negative, facultatively anaerobic coccobacilli approximately 0.4-0.5×0.