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. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

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

A novel aerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain U0301T, 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 2.0-3.0 % (w/v) NaCl. Strain U0301T shared pairwise 16S rRNA gene sequence similarities of 95.5, 95.4, 95.2 and 95.0 % to Parahaliea aestuarii S2-26T, Halioglobus pacificus KCTC 23430T, Halioglobus lutimaris HF004T and Halioglobus japonicus KCTC 23429T, respectively. Phylogenetic analysis based on the 16S rRNA gene sequences demonstrated that U0301T formed a tight phylogenetic lineage with type strains of H. pacificus and H. japonicus. The percentage of conserved protein values of strain U0301T as compared with H. japonicus KCTC 23429Tand Parahalieamediterranea 7SM29T were 62.5 and 58.0 %, respectively. The ANI values of strain U0301T with H. japonicus KCTC 23429T and P. mediterranea 7SM29T were 78.2 and 75.3 %, respectively. Both metrics of genome comparison suggested that strain U0301T showed higher homology with the genus Halioglobus than the genus Parahaliea. The strain contained ubiquinone 8 as the sole respiratory quinone. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C17 : 1ω8c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 61.7 mol%. Considering the phenotypic characteristics, chemotaxonomic data and phylogenetic analysis comprehensively, strain U0301T should represent a novel species of the genus Halioglobus, for which the name of Halioglobus sediminis sp. nov. is proposed. The type strain is U0301T (=KCTC 62082T=MCCC 1H00234T).

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

A novel strain, U0105T, 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 1.0-6.0 % (w/v) NaCl (optimum with 2.0-3.0 %), temperatures of 20-40 °C (optimum at 37 °C) and pH of 6.5-9.5 (optimum at pH 7.0-7.5). The isolate could not reduce nitrate to nitrite. It could hydrolyse starch and Tweens 20, 40 and 60, but not casein or cellulose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain U0105T belonged to the genus Alteromonas, with highest sequence similarity to Alteromonas aestuariivivens KCTC 52655T (97.1 %). The average nucleotide identity value and the digital DNA-DNA hybridization value between strain U0105T and A. aestuariivivens KCTC 52655T were 69.2 % and 21.2 %, respectively. Strain U0105T was found to contain Q-8 as the sole menaquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids were identified as phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the chromosomal DNA was 45.3 mol%. The combined genotypic and phenotypic data show that strain U0105T represents a novel species of the genus Alteromonas, for which the name Alteromonas sediminis sp. nov. is proposed. The type strain is U0105T (=KCTC 62080T=MCCC 1H00299T).

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 1.5-2.6 µm long, designated F3105T, was isolated from a marine sediment sample collected along the coast of Rongcheng, China . The growth of strain F3105T occurred on media with 1.0-8.0 % (w/v) NaCl (optimum, 2.0-3.0 %) and a pH of 6.5-9.5 (optimum, pH 7.5) at 4-45 °C (optimum, 37 °C). The phylogenetic analysis of the 16S rRNA gene and chemotaxonomic data revealed that the isolate belonged to the genus Aliidiomarina, and is closely related to Aliidiomarina shirensis (95.9 % sequence similarity). The sole isoprenoid quinone was Q-8. The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 1ω9c and iso-C17 : 0, and its polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminolipid, two unidentified lipids and two unidentified aminophospholipids. The DNA G+C content of strain F3105T was 49.5 mol%. On the basis of phenotypic distinctiveness and phylogenetic divergence, strain F3105T is considered to represent a novel species of the genus Aliidiomarina, for which the name Aliidiomarinaceleris sp. nov. is proposed. The type strain is F3105T (=MCCC 1H00223T=KCTC 52891T).

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

A Gram-stain-negative, rod-shaped bacterium (designated strain M1309T), with slow gliding motility, was isolated from marine sediment obtained off the coast of Weihai, PR China. The growth of M1309T was observed at 16-42 °C (optimum, 37 °C) and pH 6.5-8.0 (optimum, 7.0-7.5) in the presence of 2.0-6.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain represented a member of the genus Winogradskyella. M1309T exhibited the highest 16S rRNA gene sequence similarity, of 95.5 %, to Winogradskyella poriferorum JCM 12885T. Chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included iso-C15 : 0, iso-C15 : 1G and iso-C17 : 0 3-OH. The major polar lipids included phosphatidylethanolamine, two aminolipids, and three unidentified lipids. The DNA G+C content of the strain was 36.1 mol%. On the basis of phenotypic distinctiveness and phylogenetic divergence, strain M1309T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella tangerina sp. nov. is proposed. The type strain is M1309T (=KCTC 52896T=MCCC 1K03310T).

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

A Gram-stain-negative, non-motile, aerobic, curved-rod bacterium, designated as strain 2p52T, was isolated from the marine algae Gracilaria blodgettii collected off the coast of Lingshui county, in Hainan province, China. Strain 2p52T grew at 15-42 °C (optimally at 30-33 °C), at pH 6.0-10.0 (7.5-8.0) and in the presence of 1.0-8.0 % (w/v) NaCl (2.0-3.0 %). The most closely related species was Agaribacter marinus (96.5 % 16S rRNA gene sequence similarity). Phylogenetic analysis based on the sequence of the 16S rRNA gene revealed that strain 2p52T belonged to the genus Agaribacter. The novel strain contained phophatidylethanolamine and phosphatidylglycerol as the major polar lipids. The predominant isoprenoid quinine was Q-8, and the DNA G+C content was 43.2 mol%. The major cellular fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0, and C18 : 1ω7c. The phenotypic and systematic comparative analyses indicated that the isolate is representative of a novel species of the genus Agaribacter, and the name Agaribacter flavus sp. nov. is proposed. The type strain is 2p52T (=KCTC 52473T=MCCC 1H00151T).

Robiginitalea sediminis sp. nov., isolated from a sea cucumber culture pond.

A Gram-stain negative, aerobic, non-motile, orange and rod/coccoid-shaped bacterium, designated O458T, was isolated from sediment collected from a sea cucumber culture pond located in Rongcheng, Shandong province, China (122°14'E, 36°54'N). Comparative analysis of 16S rRNA gene sequences revealed that strain O458T is a member of the genus Robiginitalea and is closely related to Robiginitalea biformata (95.7% sequence similarity) and Robiginitalea myxolifaciens (94.9%). Its DNA G+C content was 55.2 mol%. The strain grew at temperatures between 15 and 45 °C (optimum 33 °C), from pH 6.5 to 8.5 (optimum pH 7.0-7.5) and between 1.0 and 6.0% (w/v) NaCl (optimum 2.0%). Strain O458T was found to contain menaquinon-6 (MK-6) as the only respiratory quinone, iso-C15:0, iso-C17:0 3-OH and Summed feature 1 (iso-C15:1 H and/or iso-C13:0 3-OH) as the major fatty acids. The major polar lipids were phosphatidylethanolamine (PE) and four unidentified lipids (L1, L2, L3 and L4). On the basis of the results of the phylogenetic and phenotypic analyses it is suggested that strain O458T represents a novel species of the genus Robiginitalea, for which the name Robiginitalea sediminis sp. nov. is proposed. The type strain is O458T (=KCTC 52898T=MCCC 1H00190T).

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

A Gram-stain-negative, facultatively anaerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain B011T, 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 B011T, Seonamhaeicola algicola (96.8 % 16S rRNA gene sequence similarity) and Seonamhaeicola aphaedonensis (95.0 %) belonged to the same clade. Optimal growth occurred in the presence of 3.0 % (w/v) NaCl, at pH 6.5-7.5 and at 28 °C. Menaquinone-6 (MK-6) was the predominant respiratory quinone. The major fatty acids (>10 %) were iso-C15 : 1 G (23.4 %) and iso-C15 : 0 (22.8 %). The major polar lipids were phosphatidylethanolamine, one aminolipid and three unknown lipids. The DNA G+C content of strain B011T was 33.9 mol%. On the basis of polyphasic analysis, strain B011T is considered to represent a novel species in the genus Seonamhaeicola, for which the name Seonamhaeicolamarinus sp. nov. is proposed. The type strain is B011T (=MCCC 1H00146T=NBRC 112333T).

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 7.0-7.5 and with 2.0-3.0 % (w/v) NaCl. The dominant cellular fatty acids of strain N62T were iso-C15 : 0, iso-C15 : 0 G, iso-C17 : 0 3-OH and iso-C17 : 1 3-OH. The major respiratory quinone was MK-6, and the DNA G+C content was 35.3 mol%. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that N62T was a member of the family Crocinitomicaceae and had a 16S rRNA gene sequence similarity of 95.8-97.2 % with recognized Brumimicrobium species. On the basis of the phylogenetic and phenotypic evidences, strain N62T represents a novel species of the genus Brumimicrobium, for which the name Brumimicrobium aurantiacum sp. nov. is proposed. The type strain is N62T (=KCTC 42589T=MCCC 1H00117T).

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

A Gram-stain-negative, strictly aerobic, non-flagellated, yellow-pigmented, rod-shaped bacterial strain, designated 0182T, 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). The strain grew optimally at 30 °C, pH 7.0-7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Cells of strain 0182T were approximately 0.9-2.5 µm in length and 0.2-0.4 µm in width. The major respiratory quinone was MK-7. The predominant cellular fatty acids were iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphoaminolipid, glycolipid, two unknown aminolipids and four unknown lipids. The DNA G+C content was approximately 35.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 0182T was phylogenetically related to members of the genus Crocinitomix and was closely related to Crocinitomix catalasitica with 94.6 % sequence similarity. On the basis of genotypic and phenotypic characteristics and phylogenetic evidence, strain 0182T is thought to represent a novel species of the genus Crocinitomix, for which the name Crocinitomix algicola sp. nov. is proposed. The type strain is 0182T (=KCTC 42868T =MCCC 1H00128T).

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 XJNYT, 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. Strain XJNYT grew at salinities of 0-4 % (w/v) and temperatures of 4-37 °C. The pH range for growth was 6.5-8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XJNYT belonged to the genus Confluentibacter and was closely related to the type strain of Confluentibacter lentus with 97.8 % similarity. The DNA G+C content was 34.5 mol%. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, anteiso-C15 : 0, iso-C15 : 0 3-OH, C17 : 0 2-OH and iso-C17 : 0 3-OH. The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. On the basis of morphological, physiological and molecular properties and phylogenetic distinctiveness, strain XJNYT represents a novel species within the genus Confluentibacter, for which the name Confluentibactercitreus sp. nov. is proposed. The type strain is XJNYT (=KCTC 52638T=MCCC 1H00183T).

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 WS2-14T, 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 WS2-14T grew optimally at 28 °C and pH 7.0-7.5, and was able to tolerate salt concentrations of 0.5-6.0 % (w/v) NaCl. Strain WS2-14T was characterized chemotaxonomically as possessing menaquinone-6 (MK-6) as the major respiratory quinone, as well as iso-C13 : 0, iso-C15 : 0 3-OH and iso-C15 : 0 as the predominant fatty acids. The DNA G+C content of strain WS2-14T was 31.2 mol%. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain WS2-14T was phylogenetically related to members of the genus Polaribacter and was closely related to Polaribacter haliotis, Polaribacter atrinae and Polaribacter sejongensis with 97.7, 97.4 and 97.0 % sequence similarities, respectively. On the basis of its phenotypic and chemotaxonomic properties, as well as phylogenetic analyses, strain WS2-14T was considered to represent a novel species of the genus Polaribacter, for which the name Polaribactertangerinus sp. nov. is proposed. The type strain is WS2-14T (=KCTC 52275T=MCCC 1H00163T).

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

A Gram-stain-negative, facultatively anaerobic coccobacilli approximately 0.4-0.5×0.5-1.1 µm, non-motile, orange-pigmented bacterial strain, designated am2T, was isolated from the coastal area of Weihai, PR China (121° 57' E, 37° 29' N). The temperature, pH and NaCl ranges for growth were 4-40 °C, pH 6.5-8.5 and 0.0-6.0 % (w/v) NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences revealed that am2T was phylogenetically related to members of the genus Algoriphagus and was closely related to Algoriphagus boritolerans, Algoriphagus namhaensis and Algoriphagus antarcticus with 96.4, 96.2 and 95.8 % sequence similarities, respectively. The quinone system contained menaquinone MK-7 as the predominant component. The dominant fatty acids were iso-C17 : 1ω9c,iso-C16 : 1H and iso-C15 : 0. The major polar lipids consisted of one phospholipid, phosphatidylethanolamine and six unknown lipids. The DNA G+C content was 40.6 mol%. On the basis of morphological, physiological and molecular properties as well as on phylogenetic distinctiveness, am2T should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus marinus sp. nov. is proposed. The type strain is am2T (=KCTC 52549T=MCCC 1H00178T).

Aquimarina rubra sp. nov., isolated from sediment of a sea cucumber culture pond.

A Gram-stain-negative, non-motile, rod-shaped, red-pigmented, facultatively anaerobic bacterium, designated SS2-9T, was isolated from sediment collected from a sea cucumber culture pond located in Rongcheng, Shandong province, China. Cells of strain SS2-9T were approximately 0.3-0.5 µm in width and 1.5-6.0 µm in length. The strain was able to grow at 10-37 °C, at pH 6.5-8.5 and in the presence of 0.5-6.0 % (w/v) NaCl. It grew optimally at 28 °C and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content was 34.5 mol% and the sole respiratory quinone was menaquinone 6 (MK-6). The predominant cellular fatty acids were C15 : 0, iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SS2-9T was phylogenetically related to members of the genus Aquimarina and was closely related to Aquimarina amphilecti 92VT (97.29 % similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SS2-9T was considered to represent a novel species of the genus Aquimarina, for which the name Aquimarina rubra sp. nov. is proposed. The type strain is SS2-9T (=KCTC 52274T=MCCC 1H00142T).

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

A novel bacterium, designated as strain HJR7T, 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 6.5-9.5 and 0.5-15.0 % (w/v), respectively. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain HJR7T belongs to the genus Marinobacter in the family Alteromonadaceae. The most closely related species were Marinobacter aromaticivorans (97.6 % 16S rRNA gene sequence similarity) and Marinobacter maritimus (97.3 % similarity). Ubiquinone 9 (Q-9) was the only respiratory quinone detected in strain HJR7T. The major fatty acids of strain HJR7T were C12 : 0, C16 : 0, C16 : 0 N alcohol, C18 : 1ω9c and C18 : 3ω6, 9, 12c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The DNA G+C content of strain HJR7T was 53.7 mol%. On the basis of phylogenetic, genotypic, phenotypic, and chemotaxonomic analyses, strain HJR7T represents a novel species within the genus Marinobacter, for which the name Marinobacter salexigens sp. nov. is proposed. The type strain is HJR7T (=KCTC 52545T=MCCC 1H00176T).

Algoriphagus resistens sp. nov., isolated from marine sediment.

Strain NH1T, a pink-pigmented, facultatively anaerobic, heterotrophic, catalase-positive and oxidase-negative, Gram-stain-negative marine bacterium, was isolated from marine sediment on the coast of Weihai, China. Cells of strain NH1T were rod-shaped, 0.8-2.0 µm in length and 0.5-1.0 µm in width. The strain was able to grow at 13-37 °C, pH 5.5-8.5, in the presence of 0.0-8.0 % (w/v) NaCl. Optimal growth was observed at 28 °C, with 3.0 % (w/v) NaCl and pH 6.5-7.0. Nitrate was reduced. The G+C content of the DNA was 41.9 mol%. The major isoprenoid quinone was MK-7 and the main cellular fatty acids (>10 %) were summed feature 3 (33.6 %) comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c, and iso-C15:0 (19.2%). The major polar lipids in strain NH1T were phosphatidylethanolamine, unidentified lipids, phospholipid and aminolipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NH1T was highly related to the type strains of Algoriphagus antarcticus (97.87 % 16SrRNA gene sequence similarity) and Algoriphagus ratkowskyi (97.56 %). On basis of the phenotypic and phylogenetic data, strain NH1T should be classified as representing a novel species of the genus Algoriphagus, for which the name Algoriphagus resistens sp. nov. is proposed. The type strain is NH1T (=MCCC 1H00140T=KCTC 52228T).

Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater.

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represented a member of the genus Colwellia and exhibited the highest sequence similarity (97.4 %) to Colwellia aestuarii SMK-10T. Average nucleotide identity (ANI) values based on draft genome sequences between strain QM50T and C. aestuarii KCTC 12480T showed a relatedness of 72.0 % (ANIb) and 85.1 % (ANIm). Cells of strain QM50T were approximately 0.3-0.6×0.8-2.5 µm in size and motile by means of a polar flagellum. Growth occurred in the presence of 1.0-6.0 % (w/v) NaCl (optimum, 2.0-3.0 %), at pH 6.5-8.5 (optimum, pH 7.0) and at 4-37 °C (optimum, 28-30 °C). Strain QM50T was found to contain ubiquinone 8 (Q-8) as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C17 : 1ω8c as the main cellular fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were found to be major polar lipids. The DNA G+C content of strain QM50T was determined to be 35.7 mol%. On the basis of phylogenetic and phenotypic data, strain QM50T represents a novel species of the genus Colwellia, for which the name Colwellia agarivorans sp. nov. is proposed. The type strain is QM50T (=KCTC 52273T=MCCC 1H00143T).

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. METHODS: In this analysis we identified international data sources from populations in the USA, England, Australia, China, the Netherlands, Canada, Ecuador, and Bangladesh with sufficient clinical and laboratory information collected between 1998 and 2020 to obtain a healthy reference sample. Individuals with clinical or biochemical evidence of a condition that could reduce haemoglobin concentrations were excluded. We estimated haemoglobin thresholds (ie, 5th centiles) for children aged 6-23 months, 24-59 months, 5-11 years, and 12-17 years, and adults aged 18-65 years (including during pregnancy) for individual datasets and pooled across data sources. We also collated findings from three large-scale genetic studies to summarise genetic variants affecting haemoglobin concentrations in different ancestral populations. FINDINGS: We identified eight data sources comprising 18 individual datasets that were eligible for inclusion in the analysis. In pooled analyses, the haemoglobin fifth centile was 104·4 g/L (90% CI 103·5-105·3) in 924 children aged 6-23 months, 110·2 g/L (109·5-110·9) in 1874 children aged 24-59 months, and 114·4 g/L (113·6-115·2) in 1839 children aged 5-11 years. Values diverged by sex in adolescents and adults. In pooled analyses, the fifth centile was 122·2 g/L (90% CI 121·3-123·1) in 1741 female adolescents aged 12-17 years and 128·2 g/L (126·4-130·0) in 1103 male adolescents aged 12-17 years. In pooled analyses of adults aged 18-65 years, the fifth centile was 119·7 g/L (90% CI 119·1-120·3) in 3640 non-pregnant females and 134·9 g/L (134·2-135·6) in 2377 males. Fifth centiles in pregnancy were 110·3 g/L (90% CI 109·5-111·0) in the first trimester (n=772) and 105·9 g/L (104·0-107·7) in the second trimester (n=111), with insufficient data for analysis in the third trimester. There were insufficient data for adults older than 65 years. We did not identify ancestry-specific high prevalence of non-clinically relevant genetic variants that influence haemoglobin concentrations. INTERPRETATION: Our results enable global harmonisation of clinical and public health haemoglobin thresholds for diagnosis of anaemia. Haemoglobin thresholds are similar between sexes until adolescence, after which males have higher thresholds than females. We did not find any evidence that thresholds should differ between people of differering ancestries. FUNDING: World Health Organization and the Bill & Melinda Gates Foundation.

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 th 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. We identified data sources from which sufficient clinical and laboratory information was available to determine an apparently healthy reference sample. Individuals were excluded if they had any clinical or biochemical evidence of a condition that may diminish haemoglobin concentration. Discrete 5 th centiles were estimated along with two-sided 90% confidence intervals and estimates combined using a fixed-effect approach. Estimates for the 5 th centile of the healthy reference population in children were similar between sexes. Thresholds in children 6-23 months were 104.4g/L [90% CI 103.5, 105.3]; in children 24-59 months were 110.2g/L [109.5, 110.9]; and in children 5-11 years were 114.1g/L [113.2, 115.0]. Thresholds diverged by sex in adolescents and adults. In females and males 12-17 years, thresholds were 122.2g/L [121.3, 123.1] and 128.2 [126.4, 130.0], respectively. In adults 18-65 years, thresholds were 119.7g/L [119.1, 120.3] in non-pregnant females and 134.9g/L [134.2, 135.6] in males. Limited analyses indicated 5 th centiles in first-trimester pregnancy of 110.3g/L [109.5, 111.0] and 105.9g/L [104.0, 107.7] in the second trimester. All thresholds were robust to variations in definitions and analysis models. Using multiple datasets comprising Asian, African, and European ancestries, we did not identify novel high prevalence genetic variants that influence haemoglobin concentration, other than variants in genes known to cause important clinical disease, suggesting non-clinical genetic factors do not influence the 5 th centile between ancestries. Our results directly inform WHO guideline development and provide a platform for global harmonisation of laboratory, clinical and public health haemoglobin thresholds.

Genomic Analysis and Characterization of Pseudotabrizicola formosa 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 XJSPT was isolated during a study of water microbial diversity in Sayram Lake, Xinjiang Province, China. Strain XJSPT was found to grow optimally at 33 °C, pH 7.5 with 1.0% (w/v) NaCl, and to produce bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequence and concatenated alignment sequences of 120 ubiquitous single-copy proteins both supported that strain XJSPT belonged to the genus Pseudotabrizicola. Both average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values were below the species delineation threshold. The primary polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unknown lipid, and one unidentified phospholipid. Based on the results of polyphasic analyses performed in this study, strain XJSPT represents a new member of the genus Pseudotabrizicola, for which the name Pseudotabrizicola formosa sp. nov. is proposed. The type strain is XJSPT (=KCTC 52636T = MCCC 1H00184T = SDUM 107003T). Comparative genomic analysis showed that four species of the genus Pseudotabrizicola shared 2570 core genes and possessed a complete anoxygenic photosystem II.