Halomonas nanhaiensis sp. nov., a halophilic bacterium isolated from a sediment sample from the South China Sea

Determination of the safety of Halomonas sp. KM-1-derived d-β-hydroxybutyric acid and its fermentation-derived impurities in mice and Japanese adults

The use of halophilic bacteria in industrial chemical and food production has received great interest because of the unique properties of these bacteria; however, their safety remains under investigation. Halomonas sp. KM-1 intracellularly stores poly-D-β-hydroxybutyric acid under aerobic conditions and successively secretes D-β-hydroxybutyric acid (D-BHB) under microaerobic conditions. Therefore, we tested the safety of Halomonas sp. KM-1-derived D-BHB and the impurities generated during D-BHB manufacturing at a 100-fold increased concentration in acute tests using mice and daily intake of 16.0 g D-BHB in Japanese adults for 12 weeks. In the mice test, there were no abnormalities in the body weights or health of mice fed the purified D-BHB or its impurities. In the Japanese adult test, blood parameters and body condition showed no medically problematic fluctuations. These findings indicate that Halomonas sp. KM-1 is safe and can be used for commercial production of D-BHB and its derivatives.

A long-awaited taxogenomic investigation of the family Halomonadaceae

The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.

Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Two novel Gram-stain-negative, facultative anaerobic, non-flagellated, rod-shaped bacterial strains, designated MT13T and MT32, were isolated from sediment samples collected from the Mariana Trench at a depth of 8300 m. The two strains grew at −2–30 °C (optimum, 25 °C), at pH 5.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 3–6 %). They did not reduce nitrate to nitrite nor hydrolyse Tweens 40 and 80, aesculin, casein, starch and DNA. The genomic G+C contents of draft genomes of strain MT13T and MT32 were 52.2 and 54.1 m ol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains MT13T and MT32 were affiliated with the genus Halomonas , with the highest similarity to the type strain of Halomonas olivaria . The values of average nucleotide identity and in silico DNA–DNA hybridization between strain MT13T and MT32, and between strain MT13T and five closely related type strains of Halomonas species indicated that strains MT13T and MT32 belonged to the same species, but represented a novel species in the genus of Halomonas . The major cellular fatty acids of strains MT13T and MT32 were C16 : 0, summed feature 3(C16 : 1  ω7c/ω6c) and summed feature 8 (C18 : 1  ω7c/ω6c). Major polar lipids of strains MT13T and MT32 included phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Ubiquinone-9 was the predominant respiratory quinone. Based on data from the present polyphasic study, strains MT13T and MT32 represent a novel species of the genus Halomonas , for which the name Halomonas profundi sp. nov. is proposed. The type strain is MT13T (=MCCC 1K06389T=KCTC 82923T).

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India

This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Intestinal mucosal microbiota composition of patients with acquired immune deficiency syndrome in Guangzhou, China

Acquired immune deficiency syndrome, caused by the human immunodeficiency virus (HIV), has been associated with intestinal dysbiosis, which includes an increase in the number of mucosa-associated pathobionts. In the present study, the intestinal mucosal microbiota patterns of HIV-infected patients were compared with those of healthy individuals in a population from Guangzhou, China. The gut microbiota of intestinal mucosal samples from 12 patients with HIV (transmission routes included sex and intravenous drug abuse) was compared with that of 12 healthy age- and sex-matched controls. Gut microbial communities were profiled via sequencing of the bacterial 16S ribosomal RNA genes. Dysbiosis in HIV-infected individuals was characterized by decreased α-diversity, decreased levels of Firmicutes and increased levels of Proteobacteria. Furthermore, low mean counts of Lachnoclostridium, Roseburia, Thauera, Dorea and Roseburia inulinivorans, and high mean counts of Halomonas and Shewanella bacteria, were indicated to be HIV-associated mucosal bacterial alterations. The relative abundance of Fusobacterium and Lachnoclostridium was significantly decreased, while that of Halomonas and Shewanella was significantly increased in patients with sexually transmitted HIV-infection compared with healthy controls. Alterations of the gut microbiota during HIV infection were also indicated to be associated with the route of HIV transmission. Certain bacteria may be potential biomarkers for HIV infection in patients from Guangzhou, China.

Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench

A piezotolerant, H₂O₂-tolerant, heavy-metal-tolerant, slightly halophilic bacterium (strain NBT06E8^T) was isolated from a deep-sea sediment sample collected from the New Britain Trench at depth of 8900 m. The strain was aerobic, motile, Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth of the strain was observed at 4-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 8-9) and in 0.5-21 % (w/v) NaCl (optimum, 3-7 %). The optimum pressure for growth was 0.1-30 MPa with tolerance up to 60 MPa. Under optimum growth conditions, the strain could tolerate 15 mM H₂O₂. Resuls of 16S rRNA gene sequence analysis showed that strain NBT06E8^T is closely related to Halomonas aquamarina DSM 30161^T (99.5%), Halomonas meridiana DSM 5425^T (99.43%) and Halomonas axialensis Althf1^T (99.35%). The digital DNA-DNA hybridization values between strain NBT06E8^T and the three related type strains, H. aquamarina, H. meridiana and H. axialensis, were 30.5±2.4 %, 30.7±2.5% and 31.5±2.5 %, respectively. The average nucleotide identity values between strain NBT06E8^T and the three related type strains were 86.26, 86.26 and 83.63 %, respectively. The major fatty acids were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and C_16 : 0. The predominant respiratory quinone detected was ubiquinone-9 (Q-9). Based on its phenotypic and phylogenetic characteristics, we conclude that strain NBT06E8^T represents a novel species of the genus Halomonas, for which the name Halomonas piezotolerans sp. nov. is proposed (type strain NBT06E8^T= MCCC 1K04228^T=KCTC 72680^T).

Biocharacteristics and draft genome sequence of Halomonas hydrothermalis C22, a pyruvate-producing halophilic bacterium isolated from a commercial Spirulina culture in Vietnam

Halophilic bacteria are receiving increasing attention for industrial chemical production processes due to their unique properties. Herein, an alkaliphilic and halophilic bacterium was isolated from a commercial Spirulina culture at Nghe An province in Vietnam and found to secrete pyruvate. Pyruvate is widely used as a starting material in the industrial biosynthesis of pharmaceuticals, and is employed for production of crop protection agents, polymers, cosmetics, and food additives. Phenotypic and chemotaxonomic characterization, and the 16S rRNA gene sequence homology with Halomonas hydrothermalis strain DSM 15,725 (99.2%) predicted that the strain belongs to the Halomonas genus, thus we named this strain as H. hydrothermalis strain C22. We investigated the biocharacteristics and capacity of strain C22 and determined the draft genome sequence comprising 3,934,166 bp with a G + C content of 60.2% encoding 3,668 proteins, 58 tRNAs, 9 rRNAs, and 1 tmRNA. Maximal pyruvate secretion reached 51.1 g/l after 84 h of cultivation. The results will facilitate future studies on the genetic and metabolic diversity of halophilic bacteria and expand our understanding of important bioprocesses in this microorganism.

Halalkalibacillus sediminis sp. nov., isolated from sediment of sea cucumber culture pond

A Gram-stain-positive, rod-shaped (0.3-0.4×1.2-2.0 µm), strictly aerobic and beige-pigmented bacterium, designated B3227^T, was isolated from the sediment of a sea cucumber culture pond in Rongcheng, China (122.2° E 36.9° N). Its biochemical characteristics analysis revealed that the cells of this bacterium were catalase-positive and oxidase-negative. Cell growth occurred at 15-45 °C (optimum, 37 °C), pH 6.5-9.0 (pH 7.5-8.0) and in the presence of 0.0-22.0 % (w/v) NaCl (6.0-9.0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain B3227^T exhibited similarities of 95.7, 95.5, 95.5 and 95.3 % to the type strains of Filobacillus milensis, Piscibacillus salipiscarius, Halalkalibacillus halophilus and Piscibacillus halophilus, respectively, and the results of physiological analyses revealed that strain B3227^T was most similar to the genus Halalkalibacillus. The cells were endospore-forming and comprised an A1-γ-meso-diaminopimelic acid-type peptidoglycan. The respiratory quinone of strain B3227^T was MK-7, and the dominant fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was 38.7 mol%. The average nucleotide identity values between strain B3227^T and H. halophilus JCM 14192^T (ANIb 69.5%, ANIm 84.2 %) and F. milensis JCM 12288^T (ANIb 70.1 %, ANIm 84.1 %) were below the cut-off level (95-96  %) for species delineation. The results of kegg analysis revealed that strain B3227^T could biosynthesize shikimate acid, a base compound for the formulation of the swine flu drug. Based on its morphological and physiological properties, as well as phylogenetic distinctiveness, strain B3227^T should be placed into the genus Halalkalibacillus as a representative of a new species, for which the name Halalkalibacillus sediminis sp. nov. is proposed. The type strain is B3227^T (=KCTC 33093^T=MCCC 1H00193^T).

Halomonas nigrificans sp. nov., isolated from cheese

A Gram-stain-negative, rod-shaped Proteobacteria isolate, MBT G8648^T, was obtained from an acid curd cheese called Quargel. The isolate was moderately salt tolerant and motile, with numerous peritrichous flagella. The 16S rRNA gene sequence analysis indicated that the strain belongs to the genus Halomonas, with 98.42 % 16S rRNA gene sequence similarity with Halomonas titanicae BH1^T as nearest related neighbour. Further comparative sequence analysis of secA and gyrB genes, as well as physiological and biochemical tests, revealed that this bacterium formed a taxon well-separated from its nearest neighbours and other established Halomonas species. Thus, the strain represents a new species, for which the name Halomonas nigrificans sp. nov. is proposed, with strain MBT G8648^T (=LMG 29097^T =DSM 105749^T) as type strain.

Halomonas shantousis sp. nov., a novel biogenic amines degrading bacterium isolated from Chinese fermented fish sauce

A Gram-negative, aerobic, short rod-shaped and non-motile bacterium, designated SWA25(T), was isolated from Chinese fermented fish sauce in Shantou, Guangdong Province, China. Strain SWA25(T) was moderately halophilic, formed colourless colonies and grew at 10-45 °C (optimum, 37 °C) and pH 4-9 (optimum, 6-7) in the presence of 0.5-22.5 % (w/v) NaCl (optimum, 3 %). The major cellular fatty acids (>10 %) were identified as C18:1 ω7C, C16:0, C16:1 ω7c, and C19:0 cyclo ω8c, and the predominant respiratory ubiquinone was Q-9. The genomic DNA G+C content was 61.3 ± 2.1 mol %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SWA25(T) belonged to the genus Halomonas in the family Halomonadaceae. The closest relatives were Halomonas xianhensis A-1(T) (96.5 % 16S rRNA gene sequence similarity), H. lutea DSM 23508(T) (96.5 %) and H. muralis LMG 20969(T) (96.1 %). DNA-DNA hybridization assays showed 30.7 ± 2.6 % relatedness between strain SWA25(T) and H. xianhensis A-1(T), and 39.4 ± 4.1 % between strain SWA25(T) and H. lutea DSM 23508(T). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SWA25(T) should be placed in the genus Halomonas as a representative of a novel species. The name Halomonas shantousis sp. nov. is proposed, with SWA25(T)(=CCTCC AB 2013151(T) = JCM 19368(T)) as the type strain.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.