Genome sequence-based species delimitation with confidence intervals and improved distance functions

A Bacillus velezensis strain isolated from oats with disease-preventing and growth-promoting properties

Endophytes have been shown to promote plant growth and health. In the present study, a Bacillus velezensis CH1 (CH1) strain was isolated and identified from high-quality oats, which was capable of producing indole-3-acetic acid (IAA) and strong biofilms, and capabilities in the nitrogen-fixing and iron carriers. CH1 has a 3920 kb chromosome with 47.3% GC content and 3776 code genes. Compared genome analysis showed that the largest proportion of the COG database was metabolism-related (44.79%), and 1135 out of 1508 genes were associated with the function "biosynthesis, transport, and catabolism of secondary metabolites." Furthermore, thirteen gene clusters had been identified in CH1, which were responsible for the synthesis of fifteen secondary metabolites that exhibit antifungal and antibacterial properties. Additionally, the strain harbors genes involved in plant growth promotion, such as seven putative genes for IAA production, spermidine and polyamine synthase genes, along with multiple membrane-associated genes. The enrichment of these functions was strong evidence of the antimicrobial properties of strain CH1, which has the potential to be a biofertilizer for promoting oat growth and disease resistance.

Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns

A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.

Genome sequence-based species classification of Enterobacter cloacae complex: a study among clinical isolates

Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, "E. xiangfangensis," "E. hoffmanii." While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates.

IMPORTANCE

Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.

Comprehensive Analysis of Antiphage Defense Mechanisms: Serovar-Specific Patterns

Leptospirosis is a major zoonotic disease caused by pathogenic spirochetes in the genus Leptospira, affecting over a million people annually and causing approximately 60,000 deaths. Leptospira interrogans, a key causative agent, likely possesses defense systems against bacteriophages (leptophages), yet these systems are not well understood. We analyzed 402 genomes of L. interrogans using the DefenseFinder tool to identify and characterize the antiphage defense systems. We detected 24 unique systems, with CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins), PrrC, Borvo, and Restriction-Modification (R-M) being the most prevalent. Notably, Cas were identified in all strains, indicating their central role in phage defense. Furthermore, there were variations in the antiphage system distribution across different serovars, suggesting unique evolutionary adaptations. For instance, Retron was found exclusively in the Canicola serovar, while prokaryotic Argonaute proteins (pAgo) were only detected in the Grippotyphosa serovar. These findings significantly enhance our understanding of Leptospira's antiphage defense mechanisms. They reveal the potential for the development of serovar-specific phage-based therapies and underscore the importance of further exploring these defense systems.

Roseinatronobacter alkalisoli sp. nov., an alkaliphilic bacterium isolated from soda soil, and genome-based reclassification of the genera Rhodobaca and Roseinatronobacter

The genera Rhodobaca and Roseinatronobacter are phylogenetically related genera within the family Paracoccaceae. Species of these genera were described using 16S rRNA gene-based phylogeny and phenotypic characteristics. However, the 16S rRNA gene identity and phylogeny reveal the controversy of the taxonomic status of these two genera. In this work, we examined the taxonomic positions of members of both genera using 16S rRNA gene phylogeny, phylogenomic analysis and further validated using overall genome-related indexes, including digital DNA-DNA hybridization, average nucleotide identity, average amino acid identity and percentage of conserved proteins. Based on phylogenetic and phylogenomic results, the current four species of the two genera clustered tightly into one clade with high bootstrap values, suggesting that the genus Rhodobaca should be merged with Roseinatronobacter. In addition, a novel species isolated from a soda soil sample collected from Anda City, PR China, and designated as HJB301T was also described. Phenotypic, chemotaxonomic, genomic and phylogenetic properties suggested that strain HJB301T (=CCTCC AB 2021113T=KCTC 82977T) represents a novel species of the genus Roseinatronobacter, for which the name Roseinatronobacter alkalisoli sp. nov. is proposed.

Clostridium omnivorum sp. nov., isolated from anoxic soil under the treatment of reductive soil disinfestation

Reductive soil disinfestation (RSD), also known as biological soil disinfestation, is a bioremediation method used to suppress soil-borne plant pathogens by stimulating the activity of indigenous anaerobic bacteria in the soil. An anaerobic bacterial strain (E14T) was isolated from an anoxic soil sample subjected to RSD treatment and then comprehensively characterized. Cells of the strain were Gram-stain-positive, curved to sigmoid, and spore-forming rods. Cells were motile with a polar flagellum. Strain E14T grew in peptone-yeast extract broth, indicating that it utilized proteinous compounds. Strain E14T was also saccharolytic and produced acetate, isobutyrate, butyrate, isovalerate and gases (H2 and CO2) as fermentation products. The strain did not decompose any of examined polysaccharides except for starch. The major cellular fatty acids of strain E14T were iso-C15:0 and iso-C15:0 DMA. The closest relative to strain E14T, based on 16S rRNA gene sequences, was Clostridium thermarum SYSU GA15002T (96.2 %) in the Clostridiaceae. Whole-genome analysis of strain E14T showed that its genome was 4.66 Mb long with a genomic DNA G+C content of 32.5 mol%. The average nucleotide identity (ANIb) between strain E14T and C. thermarum SYSU GA15002T was 69.0 %. The presence of the genes encoding glycolysis and butyrate production via the acetyl-CoA pathway was confirmed through genome analysis. Based on the obtained phylogenetic, genomic and phenotypic data, we propose that strain E14T should be assigned to the genus Clostridium in the family Clostridiaceae as Clostridium omnivorum sp. nov. The type strain is E14T (=NBRC 115133T=DSM 114974T).

Actinotalea lenta sp. nov., a novel actinomycete isolated from tidal flat sediment

Two Gram-stain-positive, aerobic, oxidase- and catalase-negative, non-motile, and short rod-shaped actinomycetes, named SYSU T00b441T and SYSU T00b490, were isolated from tidal flat sediment located in Guangdong province, PR China. The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU T00b441T and SYSU T00b490 were 99.3, 99.5 and 97.1 %, respectively. Strains SYSU T00b441T and SYSU T00b490 exhibited the highest 16S rRNA gene sequence similarities to Actinotalea ferrariae CF 5-4T (97.1 %/98.2 %), with ANI values of 74.01/73.88 % and dDDH values of 20.5/20.4 %. In the phylogenomic tree, the two isolates were affiliated with the genus Actinotalea. The genomes of strains SYSU T00b441T and SYSU T00b490 were 3.31 and 3.34 Mb, and both had DNA G+C contents of 72.8 mol%, coding 3077 and 3085 CDSs, three and three rRNA genes, and 53 and 51 tRNAs, respectively. Growth occurred at 15-40 °C (optimum, 28-30 °C), pH 4.0-10.0 (optimum, 7.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 3 %). The major fatty acids (>10  %) of strains SYSU T00b441T and SYSU T00b490 were anteiso-C15 : 0 and C16 : 0. The major respiratory quinone was identified as MK-10(H4). The polar lipids of strains SYSU T00b441T and SYSU T00b490 were diphosphatidyl glycerol, phosphatidylglycerol, phosphoglycolipid, phosphatidyl ethanolamine, two phosphatidylinositol mannosides, two glycolipids and two phospholipids. Based on these data, the two strains (SYSU T00b441T and SYSU T00b490) represent a novel species of the genus Actinotalea, for which the name Actinotalea lenta sp. nov is proposed. The type strain is SYSU T00b441T (=GDMCC 1.3827T=KCTC 49943T).

Aequorivita sediminis sp. nov. and Aequorivita marina sp. nov., isolated from marine sediment

Two Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strains, forming yellow colonies and designated F6058T and S2608T, were isolated from marine sediment collected in Weihai, PR China. Both strains grow at 4-40 °C (optimum, 30-33 °C), pH 6.0-7.5 (optimum, pH 6.5) and in the presence of 0-7.0 % (w/v) NaCl. The optimum NaCl concentrations for strains F6058T and S2608T were 2.0 % and 2.5 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains F6058T and S2608T share an evolutionary lineage with members of the genus Aequorivita. The isolates exhibited a 16S rRNA gene sequence similarity of 96.7 % to each other. Strains F6058T exhibited the highest 16S rRNA gene sequence similarity to Aequorivita xiaoshiensis F64183T (98.8 %), and S2608T was most similar to Aequorivita capsosiphonis A71T (96.9 %). Iso-C15:0, anteiso-C15:0 and iso-C17:0 3-OH were the major fatty acids of strains F6058T and S2608T. The sole respiratory quinone of both isolates was menaquinone 6 (MK-6). The polar lipid profiles of the isolates both consisted of phosphatidylethanolamine and phosphoglycolipids; however, strain F6058T exhibited one glycolipid, one aminolipid and two unidentified polar lipids, and strain S2608T also had two glycolipids and one unidentified polar lipid. The DNA G+C contents of strains F6058T and S2608T were 34.6 % and 37.7 mol%, respectively. Based on their phenotypic, chemotaxonomic and genomic characteristics, strains F6058T and S2608T were considered to represent novel species of the genus Aequorivita, for which the names Aequorivita sediminis sp. nov. and Aequorivita marina sp. nov. were proposed. The type strains are F6058T (=KCTC 92653T=MCCC 1H01358T) and S2608T (KCTC 92652T=MCCC 1H01361T).

Marortus luteolus Yu et al. 2019 is a later heterotypic synonym of Zhongshania marina On et al. 2019

Phylogeny of 16S rRNA gene sequences showed that Marortus luteolus ZX-21T and Zhongshania marina DSW25-10T are closely related, and form a monophyletic clade affiliated with the genus Zhongshania. Whole genome sequence comparisons showed that M. luteolus ZX-21T and Z. marina DSW25-10T shared 78.8 % digital DNA-DNA hybridization, 97.6 % average nucleotide identity and 98.1 % average amino acid identity. These values exceeded the recommended threshold values for species delineation. Thus, based on the principle of priority, we propose the reclassification of Marortus luteolus Yu et al. 2019 as a later heterotypic synonym of Zhongshania marina On et al. 2019.

Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids

In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.

Mangrovimonas cancribranchiae sp. nov., a novel bacterial species associated with the gills of the fiddler crab Cranuca inversa (Brachyura, Ocypodidae) from Red Sea mangroves

Two bacteria, UG2_1T and UG2_2, were isolated from the gill tissues of the mangrove fiddler crab Cranuca inversa collected on the east coast of the Red Sea (Thuwal, Saudi Arabia). The cells are Gram-negative, rod-shaped, orange-pigmented, motile by gliding with no flagella, strictly aerobic, and grow at 20-37 °C (optimum, 28-35 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0), and with 1-11 % (w/v) NaCl (optimum, 2-4 %). They were positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolates UG2_1T and UG2_2 belong to the genus Mangrovimonas, showing the highest similarity to Mangrovimonas spongiae HN-E26T (99.4 %). Phylogenomic analysis based on the whole genomes, independently using 49 and 120 concatenated genes, showed that strains UG2_1T and UG2_2 formed a monophyletic lineage in a different cluster from other type strain species within the genus Mangrovimonas. The genome sizes were 3.08 and 3.07 Mbp for UG2_1T and UG2_2, respectively, with a G+C content of 33.8 mol% for both strains. Values of average nucleotide identity and digital DNA-DNA hybridization between the strains and closely related species were 91.0 and 43.5 %, respectively. Chemotaxonomic analysis indicated that both strains had iso-C15 : 0 and iso-C15 : 1 G as dominant fatty acids, and the primary respiratory quinone was identified as MK-6. The major polar lipids comprised phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phylogenomic, genome relatedness, phenotypic, and chemotaxonomical data, the two isolates represent a novel species within the genus Mangrovimonas, with the proposed name Mangrovimonas cancribranchiae sp. nov., and the type strain UG2_1T (=KCTC 102158T=DSM 117025T).

Isolation and Characterization of Six Novel Fusobacterium necrophorum Phages

Introduction

Fusobacterium necrophorum, a human and animal pathogen, is the primary etiologic agent of bovine liver abscesses and a driving factor for prophylactic antibiotic use in the fed cattle industry. Considering calls to reduce agricultural antibiotic use, we isolated phages capable of killing F. necrophorum as an alternative or complementary biocontrol strategy.

Methods

Six novel phages (φFN37, φRTG5, φKSUM, φHugo, φPaco, and φBB) were isolated from rumen fluid or ruminal F. necrophorum isolates and subjected to host range testing on both F. necrophorum subspecies. Four F. necrophorum subspecies, necrophorum phages, were tested for cross-resistance and host growth inhibition individually and in pairs. Additionally, genomic sequencing, annotation, and analysis were performed.s.

Results

Four of six isolated phages were able to form lysogens, although all six contained lysogeny-related genes. φKSUM and φBB, did not form lysogens and were able to infect both subspecies. Four phages could infect F. necrophorum 8L1 (a liver abscess model challenge strain) in vitro. Genomic analysis showed that these phages belong to class Caudoviricetes with genome sizes ranging from 35 kbp to 111 kbp and GC values ranging from 26% to 36% and have extremely limited similarity to other deposited phage genomes infecting Fusobacterium or other genera.

Conclusions

Although all phages isolated contained sequences bearing similarities to genes implicated in lysogeny, the four selected for use in cocktails showed potential in inhibiting host growth, with several demonstrating promising attributes for biocontrol and therapeutic applications. Phage cocktails that may offer enhanced antibacterial activity were also identified, indicating the potential of some lysogenic phages to be adapted for biocontrol or therapeutic purposes when lytic phages are difficult to obtain.

Proposal for reclassification of the species Hungatella xylanolytica as Lacrimispora xylanisolvens nom. nov. and transfer of the genus Hungatella to the family Lachnospiraceae

Hungatella xylanolytica X5-1T is an anaerobic, xylan-fermenting bacterium first isolated from methane-producing cattle manure. Initially identified as Bacteroides xylanolyticus, this species was later reclassified as H. xylanolytica in 2019. Although this reclassification found support through Genome blast Distance Phylogeny analysis which placed H. xylanolytica X5-1T into the same clade as Hungatella effluvii DSM 24995T, it was contradicted by 16S rRNA gene phylogenetic analysis, which associated it with a set of misnamed Clostridium species later reassigned into the genus Lacrimispora. To ascertain its taxonomic position, comparative analyses were performed to re-examine the relationship between H. xylanolytica X5-1T and all species of the genera Hungatella and Lacrimispora. The ranges of 16S rRNA gene sequence similarity, average amino acid identity, and percentage of conserved protein prediction values were higher between H. xylanolytica X5-1T and species of the genus Lacrimispora than Hungatella. In addition, H. xylanolytica X5-1T was found to harbour genes and pathways conserved and exclusive to species within the genus Lacrimispora but not Hungatella. Essentially, in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree, H. xylanolytica X5-1T clustered into the same clade as species of the genus Lacrimispora, distinct from species of the genus Hungatella. It is thus clear that H. xylanolytica X5-1T represents a species within the genus Lacrimispora, which we propose to reclassify as Lacrimispora xylanisolvens nom. nov. Finally, based on the results from the phylogenetic and comparative analyses, the genus Hungatella was transferred to the family Lachnospiraceae.

Paenibacillus hexagrammi sp. nov., a novel bacterium isolated from the gut content of Hexagrammos agrammus

A Gram-stain-positive, aerobic bacterium, designated as YPD9-1T, was isolated from the gut contents of a spotty belly greenling, Hexagrammos agrammus, collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-C17: 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1T showed low sequence similarities to species of the genus Paenibacillus, Paenibacillus pocheonensis Gsoil 1138T (97.21 % of sequence similarity), Paenibacillus aestuarii CJ25T (97.12 %) and Paenibacillus allorhizoplanae JJ-42T (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1T formed a distinct branch among other species of the genus Paenibacillus. The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1T and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hexagrammi sp. nov. is proposed. The type strain of Paenibacillus hexagrammi is YPD9-1T (=KCTC 43424T =LMG 32988T).

Roseateles subflavus sp. nov. and Roseateles aquae sp. nov., isolated from artificial pond water and Roseateles violae sp. nov., isolated from a Viola mandshurica root

Two novel strains, designated APW6T and APW11T, were isolated from artificial pond water, and one novel strain, designated PFR6T, was isolated from a Viola mandshurica root. These strains were found to be Gram-negative, rod-shaped, motile by means of flagella, and oxidase-positive. Growth conditions of the type strains were as follows: APW6T, 15-43 °C (optimum, 28 °C), pH 6.0-12.0 (optimum, pH 7.0), with no salinity; APW11T, 4-35 °C (optimum, 25 °C), pH 6.0-11.0 (optimum, pH 9.0), with 0-1 % NaCl (w/v, optimum 0 %); PFR6T, 10-38 °C (optimum 28 °C), pH 6.0-12.0 (optimum, pH 7.0), with 0-2 % NaCl (w/v; optimum, 0 %). Strains APW6T, APW11T, and PFR6T belonged to the genus Roseateles, having the most 16S rRNA gene sequence similarity to Roseateles saccharophilus DSM 654T (98.1 %), Roseateles oligotrophus CHU3T (98.7 %), and Roseateles puraquae CCUG 52769T (98.1 %). The estimated genome sizes of APW6T, APW11T, and PFR6T were 50 50 473, 56 70 008, and 52 16 869 bp, respectively and the G+C contents were 69.5, 66, and 68.5 mol%. The digital DNA-DNA hybridization, average amino acid identity, and average nucleotide identity values among the novel strains and related taxa were all lower than 22.4, 74.7, and 78.9 %, respectively. The predominant cellular fatty acids (>10 %) of all strains were summed feature 3 (comprising C16 : 1  ω6c and/or C16 : 1  ω7c) and C16 : 0. PFR6T also had summed feature 8 (comprising C18 :  1  ω7c and/or C18 :  1  ω6c) as a major fatty acid. The polar lipid profile of all strains contained phosphatidylethanolamine, phosphoaminoglycolipid, and phosphoglycolipid. The distinct phylogenetic, physiological, and chemotaxonomic features reported in this study indicate that strains APW6T, APW11T, and PFR6T represent novel species within the genus Roseateles, for which the names Roseateles subflavus sp. nov., with the type strain APW6T (=KACC 22877T=TBRC 16606T), Roseateles aquae sp. nov., with the type strain APW11T (=KACC 22878T=TBRC 16607T), and Roseateles violae sp. nov (=KACC 23257T=TBRC 17653T) are respectively proposed.

Description of Corynebacterium hiratae sp. nov. isolated from a human tissue bone a novel member of Corynebacterium Genus

BACKGROUND

Corynebacterium spp. are widely disseminated in the environment, and they are part of the skin and mucosal microbiota of animals and humans. Reports of human infections by Corynebacterium spp. have increased considerably in recent years and the appearance of multidrug resistant isolates around the world has drawn attention.

OBJECTIVES

To describe a new species of Corynebacterium from human tissue bone is described after being misidentified using available methods.

METHODS

For taxonomic analyses, phylogenetic analysis of 16S rRNA and rpoB genes, in silico DNA-DNA hybridization, average nucleotide and amino acid identity, multilocus sequence analysis, and phylogenetic analysis based on the complete genome were used.

FINDINGS

Genomic taxonomic analyzes revealed values of in silico DNA-DNA hybridization, average nucleotide and amino acids identity below the values necessary for species characterization between the analyzed isolates and the closest phylogenetic relative Corynebacterium aurimucosum DSM 44532T.

MAIN CONCLUSIONS

Genomic taxonomic analyzes indicate that the isolates analyzed comprise a new species of the Corynebacterium genus, which we propose to name Corynebacterium hiratae sp. nov. with isolate 332T (= CBAS 826T = CCBH 35,014T) as the type strain.

Roseobacter fucihabitans sp. nov., isolated from the brown alga Fucus spiralis

A Gram-negative, aerobic, pink-pigmented, and bacteriochlorophyll a-containing bacterial strain, designated B14T, was isolated from the macroalga Fucus spiralis sampled from the southern North Sea, Germany. Based on 16S rRNA gene sequences, species of the genera Roseobacter and Sulfitobacter were most closely related to strain B14T with sequence identities ranging from 98.15 % (Roseobacter denitrificans Och 114T) to 99.11 % (Roseobacter litoralis Och 149T), whereas Sulfitobacter mediterraneus CH-B427T exhibited 98.52 % sequence identity. Digital DNA-DNA hybridization and average nucleotide identity values between the genome of the novel strain and that of closely related Roseobacter and Sulfitobacter type strains were <20 % and <77 %, respectively. The novel strain contained ubiquinone-10 as the only respiratory quinone and C18 : 1 ω7c, C16 : 0, C18 : 0, C12 : 1 ω7c, C18 : 2 ω7,13c, and C10 : 0 3-OH as the major cellular fatty acids. The predominant polar lipids of strain B14T were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The genome of strain B14T comprises a chromosome with a size of 4.5 Mbp, one chromid, and four plasmids. The genome contains the complete gene cluster for aerobic anoxygenic photosynthesis required for a photoheterotrophic lifestyle. The results of this study indicate that strain B14T (=DSM 116946T=LMG 33352T) represents a novel species of the genus Roseobacter for which the name Roseobacter fucihabitans sp. nov. is proposed.

Clostridium aquiflavi sp. nov., isolated from yellow water of Nongxiangxing baijiu in the Yibin region of China

A Gram-stain-positive, strictly anaerobic, endospore-forming and rod-shaped (0.6-0.8×2.7-13.1 µm) bacterium, designated as 5 N-1T, was isolated from a yellow water sample collected from the manufacturing process of Nongxiangxing baijiu in the Yibin region of Sichuan, PR China. Growth occurred at 15-40 °C (optimum growth at 37 °C), at pH 6.0-9.0 (optimum growth at pH 7.0) and in NaCl concentrations of 0-1 % (w/v) and ethanol concentrations of 0-2 % (v/v). The major fatty acids in strain 5 N-1T were C16 : 0, C18 : 0 and C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and one unidentified lipid. Phylogenetic analysis of its 16S rRNA gene sequence indicated that strain 5 N-1T was most closely related to Clostridium weizhouense YB-6T (97.70 %) and Clostridium uliginosum DSM 12992T (97.56 %). The average nucleotide identity and digital DNA‒DNA hybridization values between strain 5 N-1T and the above two type strains were 80.89 and 80.05 % and 25.80 and 25.30 %, respectively, which were all below the species thresholds. The genome size of strain 5 N-1T was 3.5 Mbp and the DNA G+C content was 27.5 mol%. Based on the results of phenotypic and genotypic analyses, strain 5 N-1T represents a novel species of the genus Clostridium, for which the name Clostridium aquiflavi sp. nov. is proposed. The type strain is Clostridium aquiflavi 5 N-1T (=CICC 24886T=JCM 35355T).

Nocardioides agri sp. nov., isolated from garden soil

A novel bacterial strain, designated as MAH-18T, was isolated from soil sampled in a flower garden. Cells of strain MAH-18T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18T grew at 20-40 °C, pH 6.0-8.0, and 0-1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4T (97.9 %), Nocardioides hankookensis DS-30T (97.9 %), Nocardioides aquiterrae GW-9T (97.6 %), Nocardioides soli mbc-2T (97.5 %), Nocardioides conyzicola HWE 2-02T (97.4 %), and Nocardioides mangrovi GBK3QG-3T (96.3 %). Strain MAH-18T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-18T and the closest type strains were 81.5-83.4 % and 24.4-25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18T. The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H4). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C16:0 iso and C17 : 1  ω6c. The DNA-DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18T as the type strain (=KACC 19744T=CGMCC 1.13656T).

Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus

Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.

Flavobacterium poyangense sp. nov., an ammonifying bacterium isolated from a freshwater lake

A Gram-stain-negative, aerobic, non-spore-forming, nonmotile, rod-shaped, and yellow-pigmented bacterium, designated strain JXAS1T, was isolated from a freshwater sample collected from Poyang Lake in China. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus Flavobacterium, being closest to Flavobacterium pectinovorum DSM 6368T (98.61 %). The genome size of strain JXAS1T was 4.66 Mb with DNA G+C content 35.7 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain JXAS1T and its closest relatives were below the threshold values of 95 and 70 %, respectively. The strain contained menaquinone 6 (MK-6) as the predominant menaquinone and the major polar lipids were phosphatidylethanolamine, one unidentified glycolipid, and one unidentified polar lipid. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C15 : 0, iso-C17 : 0 3OH, iso-C15 : 0 3OH, and summed feature 9 (iso-C17 : 1  ω9c and/or 10-methyl C16 : 0). Based on phylogenetic, genotypic, and phenotypic evidence, the isolated strain represents a new species in the genus Flavobacterium, and the name Flavobacterium poyangense is proposed. The type strain is JXAS1T (=GDMCC 1.1378T=KCTC 62719T).

The elite strain INPA03-11B approved as a cowpea inoculant in Brazil represents a new Bradyrhizobium species and it has high adaptability to stressful soil conditions

The strain INPA03-11BT, isolated in the 1980s from nodules of Centrosema sp. collected in Manaus, Amazonas, Brazil, was approved by the Brazilian Ministry of Agriculture as a cowpea inoculant in 2004. Since then, several studies have been conducted regarding its phenotypic, genetic, and symbiotic characteristics under axenic and field conditions. Phenotypic features demonstrate its high adaptability to stressful soil conditions, such as tolerance to acidity, high temperatures, and 13 antibiotics, and, especially, its high symbiotic efficiency with cowpea and soybean, proven in the field. The nodC and nifH phylogenies placed the INPA strain in the same clade as the species B. macuxiense BR 10303T which was also isolated from the Amazon region. The sequencing of the 16S rRNA ribosomal gene and housekeeping genes, as well as BOX-PCR profiles, showed its potential as a new species, which was confirmed by a similarity percentage of 94.7% and 92.6% in Average Nucleotide Identity with the closest phylogenetically related species Bradyrhizobium tropiciagri CNPSo1112T and B. viridifuturi SEMIA690T, respectively. dDDH values between INPA03-11BT and both CNPSo 1112T and SEMIA690T were respectively 58.5% and 48.1%, which are much lower than the limit for species boundary (70%). Therefore, we propose the name Bradyrhizobium amazonense for INPA03-11BT (= BR3301 = SEMIA6463).

Genomic dataset of a multiple-drug resistant Pseudomonas sp. strain RAC1 isolated from a flacherie infected Nistari race of Bombyx mori L

Species belonging to the genus Pseudomonas is a rod shaped Gram-negative bacteria emerged as an important silkworm pathogen with broad-level multi-drug resistance. The extensive usage of antimicrobials in sericulture farming is gradually leading to the emergence of multi-drug resistance (MDR) strains, posing a significant threat to the well-being of both Bombyx mori L. and serifarmers. Pseudomonas spp. with MDR level may gets transmitted from the infected silkworm to human handlers either via direct contact or through contaminated feces. To understand the emerging concern of antimicrobial resistance (AMR) in Pseudomonas spp. provides insights into their genomic information. Here, we present the draft genome sequence data of Pseudomonas sp. strain RAC1 isolated from a flacherie infected Nistari race of Bombyx mori L. from the silkworm rearing house of Raiganj University, India and sequenced using the Illumina NovaSeq 6000 platform. The estimated genome size of the strain was 4494347 bp with a G + C content of 63.5%. The de novo assembly of the genome generated 38 contigs with an N50 of 200 kb. Our data might help to reveal the genetic diversity, underlying mechanisms of AMR and virulence potential of Pseudomonas spp. This draft-genome shotgun project has been deposited under the NCBI GenBank accession number NZ_JAUTXS000000000.

Gemmobacter denitrificans sp. nov., a denitrifying bacterium, isolated from pond water for Litopenaeus vannamei

A novel Gram-stain-negative strain, designated JM10B15T, was isolated from pond water for Litopenaeus vannamei collected from Jiangmen City, Guangdong province, south PR China. Cells of the strain were aerobic, rod-shaped, and motile by lateral flagella. JM10B15T could grow at 15-40 °C, pH 6.0-9.5, and in 0-3.0 % NaCl, with optimal growth at 25-35 °C, pH 7.5-8.5, and in 0 % NaCl, respectively. Furthermore, this strain grew well on Reasoner's 2A agar but not on nutrient broth agar or Luria-Bertani agar. JM10B15T was a denitrifying bacterium capable of removing nitrites and nitrates, and three key functional genes, nasA, nirS, and nosZ, were identified in its genome. The results of phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that JM10B15T belonged to the genus Gemmobacter. JM10B15T showed the highest 16S rRNA sequence similarity to Gemmobacter lutimaris YJ-T1-11T (98.8 %), followed by Gemmobacter aquatilis IFAM 1031T (98.6 %) and Gemmobacter serpentinus HB-1T (98.1 %). The average nucleotide identity and digital DNA-DNA hybridization values between JM10B15T and the other type strains of genus Gemmobacter were 78.1-82.1 % and 18.4-22.1 %, respectively. The major fatty acids of strain JM10B15T were summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C18 : 1  ω7c 11-methyl. In addition, the major respiratory quinone of this novel strain was Q-10, and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, four unidentified phospholipids, three unidentified lipids, and an unidentified aminophospholipid. Results of analyses of the phylogenetic, genomic, physiological, and biochemical characteristics indicated that JM10B15T represents a novel species of the genus Gemmobacter, for which the name Gemmobacter denitrificans sp. nov. is proposed. The type strain is JM10B15T (=GDMCC 1.4148T=KCTC 8140T).

Identification and characterization of a novel α-haemolytic streptococci, Streptococcus parapneumoniae sp. nov., which caused bacteremia with pyelonephritis

OBJECTIVES

We report a case of bacteremia with pyelonephritis in an adult male with an underlying disease caused by α-hemolytic streptococci. α-Hemolytic streptococci were isolated from blood, but it was challenging to identify its species. This study aimed to characterize the causative bacterium SP4011 and to elucidate its species.

METHODS

The whole-genome sequence and biochemical characteristics of SP4011 were determined. Based on the genome sequence, phylogenetic analysis was performed with standard strains of each species of α-hemolytic streptococci. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated.

RESULTS

SP4011 showed optochin susceptibility and bile solubility, but did not react with pneumococcal omni antiserum. Phylogenetic analysis of the whole-genome sequence showed that SP4011 clustered with S. pneumoniae and S. pseodopneumoniae and was most closely related to S. pseodopneumoniae. Genomic analysis revealed that ANI and dDDH values between SP4011 and S. pseodopneumoniae were 94.0 % and 56.0 %, respectively, and between SP4011 and S. pneumoniae were 93.3 % and 52.2 %, respectively. Biochemical characteristics also showed differences between SP4011 and S. pseodopneumoniae and between SP4011 and S. pneumoniae. These results indicate that SP4011 is a novel species.

CONCLUSION

Our findings indicate that SP4011 is a novel species of the genus Streptococcus. SP4011 has biochemical characteristics similar to S. pneumoniae, making it challenging to differentiate and requiring careful clinical diagnosis. This isolate was proposed to be a novel species, Streptococcus parapneumoniae sp. nov. The strain type is SP4011T (= JCM 36068T = KCTC 21228T).

Draft genome sequence of an ubiquinone-10 producing Methylobacterium durans LRY1-08 isolated from lichen in Thailand

A ubiquitous and pink-pigmented facultatively methylotrophic bacterium, designated LRY1-08 (=JCM 33120), was isolated from a lichen in Thailand. Strain LRY1-08 and Methylobacterium durans NBRC 112876T shared 99.92 % similarity based on the 16S rRNA gene sequence. The draft genome of LRY1-08 was 5.26 Mbp with 4,952 protein-coding sequences and an average G + C content of 70.0 mol%. Comparing strain LRY1-08 to M. durans NBRC 112876T, the ANIb, ANIm, AAI, and digital DNA-DNA hybridization values were 96.29 %, 97.10 %, 96.7 %, and 82.29 %, respectively. Based on the phenotypic characteristics and genome analysis, it was identified as M. durans. Its genomic sequence data revealed the PHB and CoQ10 biosynthesis genes. Therefore, the results offer suggestions for further investigation into possible applications of this bacterium in biotechnology. The draft genome was deposited at DDBJ/EMBL/GenBank (DNA Databank of Japan/European Molecular Biology Laboratory/Genbank) (JAYEEX000000000).

A comparative analysis of phage classification methods in light of the recent ICTV taxonomic revisions

Recent ICTV taxonomy updates significantly changed phage taxonomy, yet a thorough phage classification workflow doesn't exist. This study compares six categorization tools and establishes a novel multi-method approach, combining genome similarity and specialized protein analysis. Applying the method to APEC phage P151 showed consistent categorization across platforms. A possible workflow for phage classification is proposed; offering a versatile tool for phage research and development.

Faecalibacterium taiwanense sp. nov., isolated from human faeces

Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1  ω7c and lacked C15 : 0 and C17 : 1  ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).

Genome Analysis of Multiple Polysaccharide-Degrading Bacterium Microbulbifer thermotolerans HB226069: Determination of Alginate Lyase Activity

Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from Qingge Port, Hainan, China. Results of the phylogenetic of the 16S rRNA gene and genotypic analysis indicated that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with a G+C content of 56.5%. Analysis of the predicted genes indicated that strain HB226069 encoded 161 carbohydrate-active enzymes (CAZymes), and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity of 117.4 U/mL at 50 °C, pH 7.0, and 0.05 M FeCl3, while exhibiting the best stability at 30 °C and pH 7.0. The Thin Layer Chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analyses indicated that the alginate oligosaccharides (AOSs) degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and supports its potential application in polysaccharide degradation.

TaqMan Real-Time PCR Assay for Specific Detection and Differentiation of Xanthomonas translucens pv. undulosa from Other Pathovars Targeting a Recombination Mediator Gene, recF

Bacterial leaf streak and black chaff diseases of wheat caused by Xanthomonas translucens pv. undulosa is becoming a major constraint to growers and trade since it is seedborne. Molecular tools for specific detection/differentiation of pv. undulosa are lacking. We report the development of a TaqMan real-time PCR for specific detection/identification of pv. undulosa targeting the recombination mediator gene (recF). Analysis of the complete recF (1,117 bp) sequences identified the gene as a reliable phylogenetic marker for identification of pv. undulosa, differentiating it from the other pathovars; recF-based sequence homology values among the 11 pathovars correlated well with genome-based DNA-DNA hybridization values. The discriminatory power of recF to differentiate pv. undulosa from the other pathovars is due to nucleotide polymorphic positions. We used these nucleotide polymorphisms to develop a TaqMan PCR for specific detection of pv. undulosa. The specificity of the assay was validated using 67 bacterial and fungal/oomycete strains. The selected primers and the double-quenched FAM-labeled TaqMan probe were specific for the detection of 11 pv. undulosa/secalis strains. The 56 strains of other X. translucens pathovars (n = 39) and non-Xanthomonas spp. (n = 17) did not exhibit any detectable fluorescence. Also, greenhouse-inoculated and naturally infected wheat leaf samples showed positive reactions for the presence of pv. undulosa DNA but not healthy control plants. The TaqMan assay reliably detected as low as 1-pg DNA amount and 10 colony forming units of the target pathogen per reaction. This TaqMan assay could be useful to regulatory agencies with economic benefits to wheat growers.

A Novel View on the Taxonomy of Sulfate-Reducing Bacterium 'Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov

Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.

Streptomyces chengbuensis sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla

Strain HUAS CB01T was a novel actinobacterium which was isolated from the rhizosphere soil of Cathaya argyrophylla, Chengbu Miao Autonomous County of Hunan Province, China. The strain formed well-growing substrate mycelium, diffusible pigments, and aerial mycelium, and differentiated into spiral-type spore chains composed of smooth-surface rod-shaped spores. Phylogenetic analysis on account of 16 S rRNA gene sequence demonstrated the strain HUAS CB01T was a member of the genus Streptomyces and had a close relationship with Streptomyces wuyuanensis CGMCC 4.7042 T (100%) and Streptomyces marianii ICN19T (99.86%). Genome-based comparisons indicated that strain HUAS CB01T could be distinctly different from its closest species, Streptomyces wuyuanensis CGMCC 4.7042 T, Streptomyces marianii ICN19T, with ANIm and dDDH results of 92.78% and 45.90%, 92.22% and 43.30%, respectively, far less than 96.7 and 70% cut-off points recommended for delineating species. The main cellular fatty acids concluded anteiso-C15:0, iso-C14:0, iso-C16:0, C16:0 and C16:1 2OH. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8) and the whole-cell sugars consisted of ribose and mannose. The polar lipids included phosphatidyl ethanolamine, diphosphatidylglycerol, phosphatidylglycerol, mannosides and unidentified phospholipids. According to these genotypic and phenotypic characteristics, strain HUAS CB01T can be distinguished and representative to be a novel species of the genus Streptomyces, for which the name Streptomyces chengbuensis is proposed. The type strain is HUAS CB01T ( = MCCC 1K08666T = JCM 36277 T).

Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov., Halophilic Archaea Isolated from Coastal and Inland Saline Soil

Four halophilic archaeal strains, BCD28T, BND7T, PSR21T, and PSRA2T, were isolated from coastal and inland saline soil, respectively. The 16S rRNA and rpoB' gene sequence similarities among these four strains and current species of Halomarina were 95.9-96.6% and 86.9-90.3%, respectively. Phylogenetic and phylogenomic analyses revealed that these four strains tightly cluster with the current species of the genus Halomarina. The AAI, ANI, and dDDH values among these four strains and current species of Halomarina were 65.3-68.4%, 75.8-77.7%, and 20.3-22.0%, respectively, clearly below the threshold values for species demarcation. Strains BCD28T, BND7T, PSR21T, and PSRA2T could be differentiated from the current species of Halomarina based on the comparison of diverse phenotypic characteristics. The major polar lipids of these four strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and four to five glycolipids. Phosphatidylglycerol sulfate (PGS) was only detected in strain BND7T. The phenotypic, phylogenetic, and genome-based analyses suggested that strains BCD28T (= CGMCC 1.18776T = JCM 34908T), BND7T (= CGMCC 1.18778T = JCM 34910T), PSR21T (= CGMCC 1.17027T = JCM 34147T), and PSRA2T (= CGMCC 1.17214T = JCM 34148T) represent four novel species of the genus Halomarina, for which the names Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov. are proposed.

Methylobacterium nigriterrae sp. nov., isolated from black soil

An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021T, was isolated from a black soil sample in Harbin, Heilongjiang province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Methylobacterium, and showed the highest sequence similarity to Methylobacterium segetis KCTC 62267 T (98.51%) and Methylobacterium oxalidis DSM 24028 T (97.79%). Growth occurred at 20-37℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0% (w/v) NaCl. Polar lipids comprised of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified polar lipid. The major cellular fatty acids (> 5%) were C18:0 and C18:1 ω7c and/or C18:1 ω6c. The predominant respiratory quinone was Q-10. The genomic G + C content was 68.36% based on the whole genome analysis. The average nucleotide identity (≤ 83.5%) and digital DNA-DNA hybridization (≤ 27.3%) values between strain SYSU BS000021T and other members of the genus Methylobacterium were all lower than the threshold values recommended for distinguishing novel prokaryotic species. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain SYSU BS000021T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nigriterrae sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000021T (= GDMCC 1.3814 T = KCTC 8051 T).

Whole Genome Analysis and Assessment of the Metabolic Potential of Streptomyces carpaticus SCPM-O-B-9993, a Promising Phytostimulant and Antiviral Agent

This work aimed to study the genome organization and the metabolic potential of Streptomyces carpaticus strain SCPM-O-B-9993, a promising plant-protecting and plant-stimulating strain isolated from brown semi-desert soils with very high salinity. The strain genome contains a linear chromosome 5,968,715 bp long and has no plasmids. The genome contains 5331 coding sequences among which 2139 (40.1%) are functionally annotated. Biosynthetic gene clusters (BGCs) of secondary metabolites exhibiting antimicrobial properties (ohmyungsamycin, pellasoren, naringenin, and ansamycin) were identified in the genome. The most efficient period of SCPM-O-B-9993 strain cultivation was 72 h: during this period, the culture went from the exponential to the stationary growth phase as well as exhibited excellent phytostimulatory properties and antiviral activity against the cucumber mosaic virus in tomatoes under laboratory conditions. The Streptomyces carpaticus SCPM-OB-9993 strain is a biotechnologically promising producer of secondary metabolites exhibiting antiviral and phytostimulatory properties.

Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean

Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.

Altererythrobacter litoralis sp. nov., a New Carotenoid-Producing Member of the Family Erythrobacteraceae, Isolated from a Tidal Flat Sediment

A new isolate designated as 1XM1-14T was isolated from a tidal flat sediment of Xiamen Island. The yellow-pigmented colonies and rod-shaped cells were observed. Strain 1XM1-14T could hydrolyze Tweens 20, 40, 60, aesculin, and skim milk, and was chemoheterotrophic and mesophilic, required NaCl for the growth. The 16S rRNA gene-based phylogenetic analysis indicated that strain 1XM1-14T was the most closely related to Altererythrobacter epoxidivorans CGMCC 1.7731T (97.0%), followed by other type strain of the genus Altererythrobacter with identities below 97.0%. The DNA-DNA hybridization and average nucleotide identity values between strain 1XM1-14T and its relatives of the genus Altererythrobacter were below the respective thresholds for prokaryotic species demarcation. The phylogenomic inference further revealed that strain 1XM1-14T formed a separate branch distinct from the type strains of the recognized species within the genus Altererythrobacter. The major cellular fatty acids of strain 1XM1-14T were identified as summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C17:1 ω6c, and C16:0; the profile of polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified glycolipid, and two unidentified lipids; the respiratory quinone was determined to ubiquinone-10. The genomic size and DNA G+C content of strain 1XM1-14T were 2.5 Mbp and 62.71%. The key carotenoid biosynthetic genes were determined in the genome of strain 1XM1-14T and the generated carotenoids were detected. The combined genotypic and phenotypic characteristics supported the classification of strain 1XM1-14T (= GDMCC 1.2383T = KCTC 82612T) as a novel species in the genus Altererythrobacter, for which the name Altererythrobacter litoralis sp. nov. is proposed.

Sphingomonas Immobilis sp. nov., and Sphingomonas natans sp. nov. bacteria isolated from soil

Two novel strains of bacteria, CA1-15T and BIUV-7T, were isolated from soil samples gathered in Cheonan-si, Republic of Korea, and Inje-gun, Republic of Korea, respectively. These bacteria are Gram-negative, aerobic, and non-motile. Phylogenetic evaluations, using the sequence of the 16S rRNA gene, showed that strains CA1-15T and BIUV-7T belong to a distinctive clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest similarity in their genetic makeup with representatives of the genus Sphingomonas. Strain CA1-15T was closely related to Sphingomonas echinoides NRRL B-3126T (97.8% similarity in 16S rRNA gene sequence), Sphingomonas oligophenolica JCM 12,082T (97.8%), Sphingomonas glacialis C16yT (97.6%) and Sphingomonas psychrolutea MDB1-AT (97.3%). Strain BIUV-7T was closely related to Sphingomonas nostoxanthinifaciens AK-PDB1-5T (97.0%), Sphingomonas vulcanisoli SN6-13T (96.3%), Sphingomonas naphthae DKC-5-1T (96.2%), and Sphingomonas prati W18RDT (95.7%). The optimal growth conditions for strains CA1-15T and BIUV-7T were determined to be at pH 7.0 and a temperature of 25 °C. Analysis of the cellular fatty acids of strain CA1-15T and BIUV-7T revealed that summed feature 8 (C18:1ω7c/C18:1ω6c) (60.4%), summed feature 8 (C18:1ω7c/C18:1ω6c) (62.9%) were the major component, respectively. Additionally, both strains exhibited ubiquinone Q-10 as their major respiratory quinone, and diphosphatidylglycerol (DPG), glycosphingolipid (SGL), and phosphatidylethanolamine (PE) as the major polar lipid. The genome of strain CA1-15T measures 4,133,944 bp, comprising 4,026 coding sequences (CDSs) and 46 tRNA genes. Similarly, the genome of strain BIUV-7T is 4,563,252 bp, characterized by 4,226 CDSs and 44 tRNA genes. The average nucleotide identity (ANI) analysis and digital DNA-DNA hybridization (dDDH) values between strain CA1-15T and other Sphingomonas species range from 73.2 to 79.9% and 19.4-22.9%, respectively. Comparatively, ANI and dDDH values between strain BIUV-7T and other Sphingomonas species are in the range of 72.9-76.5% and 19.3-20.9%, respectively. Based on the biochemical, chemotaxonomic, and phylogenetic analyses, it is evident that strains CA1-15T and BIUV-7T represent two novel bacterial species within the genus Sphingomonas. Accordingly, the names Sphingomonas immobilis sp. nov. and Sphingomonas natans sp. nov. are proposed. also, CA1-15T(= KCTC 92960T = NBRC 116547T) is the type strain of Sphingomonas immobilis and BIUV-7T(= KCTC 92961T = NBRC 116546T) is the type strain of Sphingomonas natans.

Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation

BACKGROUND

Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues.

RESULTS

Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L).

CONCLUSIONS

The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.

Exploring the comparative genome of rice pathogen Burkholderia plantarii: unveiling virulence, fitness traits, and a potential type III secretion system effector

This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies.

Adlercreutzia faecimuris sp. nov., producing propionate and acetate isolated from mouse feces

A novel strictly anaerobic bacterium, strain JBNU-10 T, was isolated from BALB/c mouse feces. Cells of the strain JBNU-10 T were Gram-stain positive, non-motile and rod-shaped. Optimum growth occurred at 37℃, with 1% (w/v) NaCl and at pH 7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JBNU-10 T belonged to the genus Adlercreutzia and were closely related to Adlercreutzia muris WCA-131-CoC-2 T (95.90%). The genome sequencing of strain JBNU-10 T revealed a genome size of 2,790,983 bp, a DNA G + C content of 69.4 mol%. It contains a total of 2,266 CDSs, 5 rRNA genes and 49 tRNA genes. According to the data obtained strain JBNU-10 T shared ANI value below 77.6- 67.7%, dDDH value below 23.8% with the closely type species. Strain JBNU-10 T possessed iso-C16:0 DMA, C18:1 CIS 9 FAME, and C18:0 DMA as the major fatty acids and had DMMK-6. The major end products of fermentation is propionate and acetate. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JBNU-10 T represent a novel species of the genus Adlercreutzia. The type strain is JBNU-10 T (= KCTC 25028 T = CCUG 75610 T).

Paracoccus benzoatiresistens sp. nov., a benzoate resistance and selenite reduction bacterium isolated from wetland

A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6T, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37 °C (optimum, 30 °C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6T belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2T with 98.1% similarity, Paracoccus fontiphilus MVW-1 T (97.9%), Paracoccus everestensis S8-55 T (97.7%), Paracoccus subflavus GY0581T (97.6%), Paracoccus sediminis CMB17T (97.3%), Paracoccus caeni MJ17T (97.0%), and Paracoccus angustae E6T (97.0%). The genome size of strain EF6T was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6T and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C18:1 ω6c and/or C18:1 ω7c) and C18:1 (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6T displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6T possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6T a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6T is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6T (= GDMCC 1.3400 T = JCM 35642 T = MCCC 1K08702T).

Reclassification of Some Exiguobacterium Species Based on Genome Analysis

The Exiguobacterium genus comprises Gram-stain-positive and facultatively anaerobic bacteria. Some Exiguobacterium species have previously shown significant high 16S rRNA gene sequence similarities with each other. This study evaluates the taxonomic classification of those Exiguobacterium species through comprehensive genome analysis. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were determined for various Exiguobacterium species pairs. The ANI and dDDH values between Exiguobacterium enclense and Exiguobacterium indicum, Exiguobacterium aquaticum and Exiguobacterium mexicanum, Exiguobacterium soli and Exiguobacterium antarcticum, and Exiguobacterium sibiricum and Exiguobacterium artemiae were above the cut-off level (95-96% for ANI and 70% for dDDH) for species delineation. Based on the findings, we propose to reclassify Exiguobacterium enclense as a later heterotypic synonym of Exiguobacterium indicum, Exiguobacterium aquaticum as a later heterotypic synonym of Exiguobacterium mexicanum, Exiguobacterium soli as a later heterotypic synonym of Exiguobacterium antarcticum and Exiguobacterium sibiricum as a later heterotypic synonym of Exiguobacterium artemiae.

Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island

Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.

Redefining piscine lactococcosis

Piscine lactococcosis is a significant threat to cultured and wild fish populations worldwide. The disease typically presents as a per-acute to acute hemorrhagic septicemia causing high morbidity and mortality, recalcitrant to antimicrobial treatment or management interventions. Historically, the disease was attributed to the gram-positive pathogen Lactococcus garvieae. However, recent work has revealed three distinct lactococcosis-causing bacteria (LCB)-L. garvieae, L. petauri, and L. formosensis-which are phenotypically and genetically similar, leading to widespread misidentification. An update on our understanding of lactococcosis and improved methods for identification are urgently needed. To this end, we used representative isolates from each of the three LCB species to compare currently available and recently developed molecular and phenotypic typing assays, including whole-genome sequencing (WGS), end-point and quantitative PCR (qPCR) assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), API 20 Strep and Biolog systems, fatty acid methyl ester analysis (FAME), and Sensititre antimicrobial profiling. Apart from WGS, sequencing of the gyrB gene was the only method capable of consistent and accurate identification to the species and strain level. A qPCR assay based on a putative glycosyltransferase gene was also able to distinguish L. petauri from L. garvieae/formosensis. Biochemical tests and MALDI-TOF MS showed some species-specific patterns in sugar and fatty acid metabolism or protein profiles but should be complemented by additional analyses. The LCB demonstrated overlap in host and geographic range, but there were relevant differences in host specificity, regional prevalence, and antimicrobial susceptibility impacting disease treatment and prevention.

IMPORTANCE

Lactococcosis affects a broad range of host species, including fish from cold, temperate, and warm freshwater or marine environments, as well as several terrestrial animals, including humans. As such, lactococcosis is a disease of concern for animal and ecosystem health. The disease is endemic in European and Asian aquaculture but is rapidly encroaching on ecologically and economically important fish populations across the Americas. Piscine lactococcosis is difficult to manage, with issues of vaccine escape, ineffective antimicrobial treatment, and the development of carrier fish or biofilms leading to recurrent outbreaks. Our understanding of the disease is also widely outdated. The accepted etiologic agent of lactococcosis is Lactococcus garvieae. However, historical misidentification has masked contributions from two additional species, L. petauri and L. formosensis, which are indistinguishable from L. garvieae by common diagnostic methods. This work is the first comprehensive characterization of all three agents and provides direct recommendations for species-specific diagnosis and management.

An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia

In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems.

IMPORTANCE

While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.

Comparative genomics of Vibrio toranzoniae strains

Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade, originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at genome level among strains, as well as to determine their phylogeny. For this purpose, whole genomes were sequenced by different technologies and the resulting sequences corrected. Genomes were annotated and compared with different online tools. Furthermore, the study of core and pan genome was examined, and the phylogeny was inferred. The content of the core genome ranged from 2,953 to 2,766 genes and that of the pangenome from 6,278 to 6,132, depending on the tool used. The comparison revealed that although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI higher than 97%,notable differences were found related to motility, capsule synthesis, iron acquisition system or mobile genetic elements. The phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle, but that of the pangenome pointed out certain geographical isolation in the same growing area. The study led to a reclassification of some isolates formerly described as V. toranzoniae and manifested the importance of cured deposited sequences to proper phylogenetic assignment.

Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil

A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 μmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).

Pradimicin U, a promising antimicrobial agent isolated from a newly found Nonomuraea composti sp. nov

Pradimicin U is a new dihydrobenzo[a]naphthacenequinone compound found to be active on a screen designed to investigate compounds with antimicrobial activity, produced by the actinomycete designated strain FMUSA5-5T. The strain was isolated from a bio-fertilizer of Musa spp. collected from Suphanburi province, Thailand. The chemotaxonomic characteristics and 16S rRNA gene analysis revealed that strain FMUSA5-5T is a member of the genus Nonomuraea. Low genome-based taxonomic criteria, average nucleotide identity (ANI) (82.8-88.3%), average amino-acid identity (AAI) (79.4-87.3%), and digital DNA-DNA hybridization (dDDH) (29.5-38.5%) values and several phenotypic differences between strain FMUSA5-5T and its closest type strains of the genus Nonomuraea indicated that strain FMUSA5-5T represents a novel species of the genus Nonomuraea and the name Nonomuraea composti sp. nov. is proposed for the strain. The crude extract from the culture broth of strain FMUSA5-5T displayed promising antimicrobial activity against several pathogens and led to the isolation of a novel secondary metabolite, pradimicin U. Interestingly, this compound displayed a broad spectrum of biological activities such as antimalarial activity against Plasmodium falciparum K1 (IC50 value = 3.65 µg/mL), anti-Mycobacterium tuberculosis H37Ra (MIC value = 25.0 µg/mL), anti-Alternaria brassicicola BCC 42724 (MIC value = 25.0 µg/mL), anti-Bacillus cereus ATCC 11778 and anti-Staphylococcus aureus ATCC 29213 (MIC values = 6.25 and 1.56 µg/mL, respectively). Moreover, the compound possessed strong anti-human small cell lung cancer (NCI-H187) activity with IC50 value of 5.69 µg/mL, while cytotoxicity against human breast cancer (MCF-7) and Vero cells was very weak (IC50 values of 52.49 and 21.84 µg/mL, respectively).

Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135

The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.