Remarkable increase in the detection and molecular characterization of adenovirus F41 in children with acute gastroenteritis in Japan, 2017-2023.

Human adenovirus (HAdV) is one of the causative viruses of acute gastroenteritis (AGE) in children worldwide. Species F is known to be enteric adenovirus (genotypes 40 and 41) detected in stool samples. In Japan, we conducted an epidemiological study and molecular characterization of HAdV before and after the COVID-19 pandemic from 2017 to 2023. Among 821 patients, HAdV was detected in 118 AGE cases (14.4%). During a period of 6 years, the HAdV detection rates for each year were relatively low at 3.7% and 0%, in 2017-2018, and 2020-2021, respectively. However, the detection rate increased to remarkably high rates, ranging from 13.3% to 27.3% in the other 4-year periods. Of these HAdV-positive strains, 83.1% were F41 genotypes and 16.9% were other genotypes (A31, B3, C1, C2/C6, and C5). Phylogenetic analyses of the nucleotide and deduced amino acid sequences of the full-length hexon gene demonstrated that HAdV-F41 strains were comprised of three clades, and each clade was distributed across the study period from 2017 to 2023. Analysis of deduced amino acid sequences of the hexon gene of the representative HAdV-F41 strains from each clade revealed numerous amino acid substitutions across hypervariable regions (HVRs) from HVR-1 to HVR-7, two insertions in HVR-1 and HVR-7, and two deletions in HVR-1 and HVR-2 of the hexon gene compared to those of the prototype strain, particularly, those of clade 3 HAdV-F41 strains. The findings suggested that the HAdV-F41 of each clade was stable, conserved, and co-circulated for over two decades in Japan.

Sphingobium cyanobacteriorum sp. nov., isolated from fresh water.

A novel Gram-stain-negative, yellow-pigmented, short rod-shaped bacterial strain, HBC34T, was isolated from a freshwater sample collected from Daechung Reservoir, Republic of Korea. The results of 16S rRNA gene sequence analysis indicated that HBC34T was affiliated with the genus Sphingobium and shared the highest sequence similarity to the type strains of Sphingobium vermicomposti (98.01 %), Sphingobium psychrophilum (97.87 %) and Sphingobium rhizovicinum (97.59 %). The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between HBC34T and species of the genus Sphingobium with validly published names were below 84.01 and 28.1 %, respectively. These values were lower than the accepted species-delineation thresholds, supporting its recognition as representing a novel species of the genus Sphingobium. The major fatty acids (>10 % of the total fatty acids) were identified as summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The main polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and two unidentified polar lipids. The respiratory quinone was Q-10. The genomic DNA G+C content of HBC34T was 64.04 %. The polyphasic evidence supports the classification of HBC34T as the type strain of a novel species of the genus Sphingobium, for which the name Sphingobium cyanobacteriorum sp. nov is proposed. The type strain is HBC34T (= KCTC 8002T= LMG 33140T).

Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae.

Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera 'Chryseosolibacter', 'Dawidia', and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.

Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic.

The taxonomic position of three actinobacterial strains, BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T, recovered from bare soil in the Sokolov Coal Basin, Czech Republic, was established using a polyphasic approach. The multilocus sequence analysis based on 100 single-copy genes positioned BCCO 10_0061T in the same cluster as Lentzea waywayandensis, strain BCCO 10_0798T in the same cluster as Lentzea flaviverrucosa, Lentzea californiensis, Lentzea violacea, and Lentzea albidocapillata, and strain BCCO 10_0856T clustered together with Lentzea kentuckyensis and Lentzea alba. Morphological and chemotaxonomic characteristics of these strains support their assignment to the genus Lentzea. In all three strains, MK-9(H4) accounted for more than 80 % of the isoprenoid quinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell sugars were rhamnose, ribose, mannose, glucose, and galactose. The major fatty acids (>10 %) were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, methyl-phosphatidylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The genomic DNA G+C content of strains (mol%) was 68.8 for BCCO 10_0061T, 69.2 for BCCO 10_0798T, and 68.5 for BCCO 10_0856T. The combination of digital DNA-DNA hybridization results, average nucleotide identity values and phenotypic characteristics of BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T distinguishes them from their closely related strains. Bioinformatic analysis of the genome sequences of the strains revealed several biosynthetic gene clusters (BGCs) with identities >50 % to already known clusters, including BGCs for geosmin, coelichelin, ε-poly-l-lysine, and erythromycin-like BGCs. Most of the identified BGCs showed low similarity to known BGCs (<50 %) suggesting their genetic potential for the biosynthesis of novel secondary metabolites. Based on the above results, each strain represents a novel species of the genus Lentzea, for which we propose the name Lentzea sokolovensis sp. nov. for BCCO 10_0061T (=DSM 116175T), Lentzea kristufekii sp. nov. for BCCO 10_0798T (=DSM 116176T), and Lentzea miocenica sp. nov. for BCCO 10_0856T (=DSM 116177T).

Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan.

Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.

Microbaculum marinisediminis sp. nov., isolated from marine sediment.

A novel Gram-stain-negative and facultatively anaerobic bacterium, designated A6E488T, was isolated from intertidal sediment collected from Xiaoshi Island, Weihai, PR China (122° 1' E 37° 31' N). Cells of strain A6E488T were rod-shaped with widths of 0.3-0.4 µm and lengths of 1.1-1.8 µm. The optimal growth conditions were determined to be in 1 % (w/v) NaCl, at 37 °C, and at pH 7.0. The predominant fatty acids (≥10 %) were C19 : 0 cyclo ω8c (59.7 %) and summed feature 8 (13.8 %, C18 : 1 ω7c and/or C18 : 1 ω6c). The sole isoprenoid quinone was Q-10. Oxidase activity was negative but catalase activity was positive. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified glycolipid, and one unidentified lipid. Based on phylogenetic analysis of 16S rRNA gene sequences, strain A6E488T showed the highest sequence similarity to Microbaculum marinum MCCC 1K03192T (97.6 %). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain A6E488T and M. marinum MCCC 1K03192T did not exceed 78 and 22 %, respectively. These values are below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation. On the basis of gene annotation, it was observed that strain A6E488T possesses the capability for thiosulphate oxidation, suggesting that this strain might be important in the sulphur cycle. Based on the results of phenotypic, genotypic, and chemical characterization, strain A6E488T is considered to represent a novel species of the genus Microbaculum, for which the name Microbaculum marinisediminis sp. nov. is proposed. The type strain is A6E488T (=KCTC 92197T=MCCC 1H00516T).

KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost.

Long reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools. Here we introduce KSNP, an efficient haplotype construction tool based on the de Bruijn graph (DBG). KSNP leverages the ability of DBG in handling high-throughput erroneous reads to tackle the challenges. Compared to other notable tools in this field, KSNP achieves at least 5-fold speedup while producing comparable haplotype results. The time required for assembling human haplotypes is reduced to nearly the data-in time.

The novel HLA-DPB1*1500:01N allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-DPB1*1500:01N differs from HLA-DPB1*05:01:01:01 by one nucleotide in exon 3.

Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant.

An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5-7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74-99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.

Paenibacillus thermotolerans sp. nov., isolated from a hot spring in Yunnan Province, south-west China.

Two Gram-positive, rod-shaped, endospore-forming strains, YIM B05601 and YIM B05602T, were isolated from soil sampled at Hamazui hot spring, Tengchong City, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Paenibacillus, appearing most closely related to Paenibacillus alkalitolerans YIM B00362T (96.9 % sequence similarity). Genome-based phylogenetic analysis confirmed that strains YIM B05601 and YIM B05602T formed a distinct phylogenetic cluster within the genus Paenibacillus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains YIM B05601 and YIM B05602T with the related species P. alkalitolerans YIM B00362T were within the ranges of 74.43-74.57 % and 12.1-18.5 %, respectively, which clearly indicated that strains YIM B05601, YIM B05602T represented a novel species. Strains YIM B05601 and YIM B05602T exhibited 99.6 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 99.8 and 100 %, respectively, suggesting that they belong to the same species. Optimum growth for both strains occurred at pH 7.0 and 45 °C. The diagnostic diamino acid in the cell-wall peptidoglycan of strains YIM B05601 and YIM B05602T was meso-diaminopimelic acid. MK-7 was the predominant menaquinone. The polar lipids of strain YIM B05602T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, four unidentified glycolipids, an unidentified polarlipid and phosphatidylinositol mannoside. The major fatty acids of the two stains were iso-C15 : 0 and anteiso-C15 : 0. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strains YIM B05601 and YIM B05602T could be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus thermotolerans sp. nov. is proposed. The type strain is YIM B05602T (=CGMCC 1.60051T=KCTC 43460T=NBRC 115924T).

Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.

Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

Chelativorans salis sp. nov., a slightly halophilic bacterium isolated from an enrichment system with saline lake sediment.

A Gram-stain-negative, non-motile, and slightly halophilic alphaproteobacterium, designated strain EGI FJ00035T, was isolated from enrichment sediment samples of a saline lake in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using the polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain EGI FJ00035T formed a distinct clade with 'Chelativorans alearense' UJN715 and 'Chelativorans xinjiangense' lm93 with sequence similarities of 98.44 and 98.22 %, respectively, while sharing less than 96.7 % with other valid type strains. The novel isolate could be distinguished from other species of the genus Chelativorans by its distinct phenotypic, physiological, and genotypic characteristics. Optimal growth of strain EGI FJ00035T occurred on marine agar 2216 at pH 7.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>5 %) were C19 : 0 cyclo ω8c, summed feature 8 (C17 : 1 ω6c and/or C17 : 1 ω7c), C16 : 0, C18 : 0, and iso-C17 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipids, unidentified glycolipids, and an unidentified lipid. Based on its genome sequence, the G+C content of strain EGI FJ00035T was 63.2 mol%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values of strain EGI FJ00035T against related members of the genus Chelativorans were below the thresholds for delineation of a novel species. According our polyphasic taxonomic data, strain EGI FJ00035T represents a new species of the genus Chelativorans, for which the name Chelativorans salis sp. nov. is proposed. The type strain of the proposed novel isolate is EGI FJ00035T (=KCTC 92251T=CGMCC 1.19480T).

Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil.

A Gram-stain-negative, rod-shaped, indole-producing, and cellulose-degrading bacterial strain, designated NEAU-G-C5T, was isolated from soil collected from a forest in Dali city, Yunnan province, south China. 16S rRNA gene sequence analysis showed that strain NEAU-G-C5T was assigned to the genus Massilia and showed high sequence similarities to Massilia phosphatilytica 12-OD1T (98.32 %) and Massilia putida 6 NM-7T (98.41 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-G-C5T formed a lineage related to M. phosphatilytica 12-OD1T and M. putida 6 NM-7T. The major fatty acids of the strain were C16 : 0, C16 : 1 ω7c, and C17 : 0 cyclo. The respiratory quinone was Q-8. The polar lipid profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. In addition, the average nucleotide identity values between strain NEAU-G-C5T and its reference strains M. phosphatilytica 12-OD1T, M. putida 6 NM-7T, M. norwichensis NS9T, and M. kyonggiensis TSA1T were 89.7, 88.2, 81.3, and 88.0 %, respectively, and the levels of digital DNA-DNA hybridization between them were found to be 58.5 % (54.9-62.0 %), 53.2 % (49.8-56.7 %), 31.9 % (28.6-35.5 %), and 57.7 % (54.1-61.2 %), respectively, which were lower than the accepted threshold values of 95-96 % and 70 %, respectively. The DNA G+C content of strain NEAU-G-C5T was 66.5 mol%. The strain could produce indoleacetic acid and cellulase. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, we conclude that strain NEAU-G-C5T represents a novel species of the genus Massilia, for which the name Massilia luteola sp. nov. is proposed. The type strain is NEAU-G-C5T (=MCCC 1K08668T=KCTC 8080T).

Genome-based reclassification of Salipiger manganoxidans (Rajasabapathy et al. 2016) Wirth et al. 2018 as a later heterotypic synonym of Salipiger marinus (Lai et al. 2011) Wirth et al. 2018.

Salipiger manganoxidans VSW210T was compared with Salipiger marinus CK-I3-6T to examine the taxonomic relationship between the two type strains. In phylogenetic trees drawn using whole genome sequences and 16S rRNA gene sequences, S. manganoxidans VSW210T and S. marinus CK-I3-6T clade together and showed a 99.6 % 16S rRNA sequence similarity. The average amino acid identity (AAI), average nucleotide identity (ANIb and ANIm) and digital DNA-DNA hybridization (dDDH) values between S. manganoxidans VSW210T and S. marinus CK-I3-6T were below 97.5, 97.4, 98.4 and 85.1±2.5 %, respectively, all of which were greater than the species delineation threshold AAI value (95.5 %), ANI value (95-96 %) and dDDH value (70 %). Most phenotypic features between both species were almost identical, although there were some differences. The present results show that Salipiger manganoxidans is a later heterotypic synonym of Salipiger marinus.

Achromobacter seleniivolatilans sp. nov. and Buttiauxella selenatireducens sp. nov., isolated from the rhizosphere of selenium hyperaccumulator Cardamine hupingshanesis.

Two Gram-stain-negative bacterial strains, R39T and R73T, were isolated from the rhizosphere soil of the selenium hyperaccumulator Cardamine hupingshanesis in China. Strain R39T transformed selenite into elemental and volatile selenium, whereas strain R73T transformed both selenate and selenite into elemental selenium. Phylogenetic and phylogenomic analyses indicated that strain R39T belonged to the genus Achromobacter, while strain R73T belonged to the genus Buttiauxella. Strain R39T (genome size, 6.68 Mb; G+C content, 61.6 mol%) showed the closest relationship to Achromobacter marplatensis LMG 26219T and Achromobacter kerstersii LMG 3441T, with average nucleotide identity (ANI) values of 83.6 and 83.4 %, respectively. Strain R73T (genome size, 5.22 Mb; G+C content, 50.3 mol%) was most closely related to Buttiauxella ferragutiae ATCC 51602T with an ANI value of 86.4 %. Furthermore, strain A111 from the GenBank database was found to cluster with strain R73T within the genus Buttiauxella through phylogenomic analyses. The ANI and digital DNA-DNA hybridization values between strains R73T and A111 were 97.5 and 80.0% respectively, indicating that they belong to the same species. Phenotypic characteristics also differentiated strain R39T and strain R73T from their closely related species. Based on the polyphasic analyses, strain R39T and strain R73T represent novel species of the genera Achromobacter and Buttiauxella, respectively, for which the names Achromobacter seleniivolatilans sp. nov. (type strain R39T=GDMCC 1.3843T=JCM 36009T) and Buttiauxella selenatireducens sp. nov. (type strain R73T=GDMCC 1.3636T=JCM 35850T) are proposed.

Refining the taxonomy of the order Hyphomicrobiales (Rhizobiales) based on whole genome comparisons of over 130 type strains.

The alphaproteobacterial order Hyphomicrobiales consists of 38 families comprising at least 152 validly published genera as of January 2024. The order Hyphomicrobiales was first described in 1957 and underwent important revisions in 2020. However, we show that several inconsistencies in the taxonomy of this order remain and we argue that there is a need for a consistent framework for defining families within the order. We propose a common genome-based framework for defining families within the order Hyphomicrobiales, suggesting that families represent monophyletic groups in core-genome phylogenies that share pairwise average amino acid identity values above ~75 % when calculated from a core set of 59 proteins. Applying this framework, we propose the formation of four new families and to reassign the genera Salaquimonas, Rhodoblastus, and Rhodoligotrophos into Salaquimonadaceae fam. nov., Rhodoblastaceae fam. nov., and Rhodoligotrophaceae fam. nov., respectively, and the genera Albibacter, Chenggangzhangella, Hansschlegelia, and Methylopila into Methylopilaceae fam. nov. We further propose to unify the families Bartonellaceae, Brucellaceae, Phyllobacteriaceae, and Notoacmeibacteraceae as Bartonellaceae; the families Segnochrobactraceae and Pseudoxanthobacteraceae as Segnochrobactraceae; the families Lichenihabitantaceae and Lichenibacteriaceae as Lichenihabitantaceae; and the families Breoghaniaceae and Stappiaceae as Stappiaceae. Lastly, we propose to reassign several genera to existing families. Specifically, we propose to reassign the genus Pseudohoeflea to the family Rhizobiaceae; the genera Oricola, Roseitalea, and Oceaniradius to the family Ahrensiaceae; the genus Limoniibacter to the emended family Bartonellaceae; the genus Faunimonas to the family Afifellaceae; and the genus Pseudochelatococcus to the family Chelatococcaceae. Our data also support the recent proposal to reassign the genus Prosthecomicrobium to the family Kaistiaceae.

Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing.

This review highlights operational principles, features, and modern aspects of the development of third-generation sequencing technology of biopolymers focusing on the nucleic acids analysis, namely the nanopore sequencing system. Basics of the method and technical solutions used for its realization are considered, from the first works showing the possibility of creation of these systems to the easy-to-handle procedure developed by Oxford Nanopore Technologies company. Moreover, this review focuses on applications, which were developed and realized using equipment developed by the Oxford Nanopore Technologies, including assembly of whole genomes, methagenomics, direct analysis of the presence of modified bases.

Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation.

BACKGROUND: Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations. RESULTS: Based on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability. CONCLUSIONS: Analysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.

Proposal of Shuttleworthella gen. nov. and Nostocoides gen. nov. as replacement names for the illegitimate prokaryotic generic names Shuttleworthia and Tetrasphaera, respectively.

The prokaryotic generic name Shuttleworthia Downes et al. 2002 is illegitimate because it is a later homonym of the plant genus Shuttleworthia Meisner 1840 and the mollusk genus Shuttleworthia Baker 1941 (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Shuttleworthella, with type species Shuttleworthella satelles comb. nov. The prokaryotic generic name Tetrasphaera Maszenan et al. 2000 is illegitimate because it is a later homonym of Tetrasphaera Popofsky 1913 (Protozoa, Radiolaria) and of Tetrasphaera Górka 1965 (a fossil dinoflagellate) (Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Nostocoides, with type species Nostocoides japonicum comb. nov.