Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera

Evidence that ribosomal protein bS21 is a component of the OLE ribonucleoprotein complex

OLE RNAs represent a large and highly structured noncoding RNA (ncRNA) class that is mostly found in Gram-positive extremophiles and/or anaerobes of the Bacillota phylum. These ~600-nucleotide RNAs are among the most structurally complex and well-conserved large ncRNAs whose precise biochemical functions remain to be established. In Halalkalibacterium halodurans, OLE RNA is involved in the adaptation to various unfavourable growth conditions, including exposure to cold (≤20°C), ethanol (≥3% [v/v]), excess Mg2+ (≥4 mM), and non-glucose carbon/energy sources. OLE forms a ribonucleoprotein (RNP) complex with the OLE-associated proteins A, B and C, which are known to be essential for OLE RNP complex function in this species. Bacteria lacking OLE RNA (Δole) or a functional OLE RNP complex exhibit growth defects under the stresses listed above. Here, we demonstrate that ribosomal protein bS21 is a natural component of the OLE RNP complex and we map its precise RNA binding site. The presence of bS21 results in a conformational change in OLE RNA resembling a k-turn substructure previously reported to be relevant to the function of the OLE RNP complex. Mutational disruption of the bS21 protein or its OLE RNA binding site results in growth inhibition under cold and ethanol stress to the same extent as the deletion of the gene for OLE RNA. These findings are consistent with the hypothesis that bS21 is a biologically relevant component of the OLE RNP complex under a subset of stresses managed by the OLE RNP complex.

Molecular basis of protein-DNA interactions between Halalkalibacterium halodurans MntR and its DNA operator sequence

Transition metals such as iron, zinc and manganese are essential for bacterial survival. A pivotal role in regulation of manganese homeostasis in bacterium Halalkalibacterium halodurans has MntR protein (HhMntR). In this work, molecular dynamics simulations of holoprotein (with Mn2+) and apoprotein (without Mn2+) HhMntR in complex with DNA mntA operator were conducted and enabled understanding of interaction between HhMntR and DNA on molecular level. Molecular mechanism through which affinity of HhMntR towards DNA is increased upon Mn2+ binding was revealed. Holoprotein binds DNA through stable and consistent noncovalent interactions, while apoprotein shows highly dynamic behavior, attaching to and detaching from the DNA backbone and inner grooves on a nanosecond time scale. The same observations are seen even during the simulations that started with protein and DNA separated from the complex. Additionally, key amino acids involved in the formation of the HhMntR-DNA complex were identified, leading to the proposal of a molecular framework that allows HhMntR to perform its biological function as a transcription factor. Overall, observed behaviors promote the lateral movement of HhMntR along the DNA sequence, enabling the protein to remain close to the DNA while it seeks out specific base pairs for strong binding upon activation by Mn2+.

Genomic insights into novel predatory myxobacteria isolated from human feces

Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35T and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35T. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.

Phylogenomic studies and molecular markers clarifying the evolutionary relationships and classification of Pseudalkalibacillus species: proposal for the family Guptibacillaceae fam. nov. harbouring the genera Guptibacillus gen. nov. and Exobacillus gen. nov

The genus Pseudalkalibacillus, created by the reclassification of specific deep-branching Alkalihalobacillus species, exhibits polyphyletic branching. The Genome Taxonomy Database (GTDB) also assigns Pseudalkalibacillus species into two families and three genera. To clarify the evolutionary relationships and classification of Pseudalkalibacillus species, we report detailed investigations using phylogenomic and molecular signature-based approaches. In phylogenomic trees, Pseudalkalibacillus species are distributed within two family-level lineages. One of these clades, containing the type species of Pseudalkalibacillus (viz. Pseudalkalibacillus decolorationis), represents the genus Pseudalkalibacillus, groups within the family Fictibacillaceae. Ten novel conserved signature indels (CSIs) identified in this study are specific for this clade, providing a robust means for the differentiation of the emended genus Pseudalkalibacillus. The remaining Pseudalkalibacillus species form a separate family-level clade, designated as f_HBI72195 in the GTDB. Within this clade, all species except Pseudalkalibacillus caeni form a robust clade designated as Pseudalkalibacillus clade -2 in our work and g_Anaerobacillus_A in the GTDB. We have also identified 15 novel CSIs specific to this clade. As the Pseudalkalibacillus clade -2 is distinct from Pseudalkalibacillus, we propose transferring species from this clade into a new genus, Guptibacillus gen. nov. The species P. caeni branches distinctly from other Pseudalkalibacillus species, and the GTDB considers it a novel genus (g_Bacillus_BR). Six newly identified CSIs are specific to this species, and we are proposing the transfer of this species into a new genus, Exobacillus gen. nov. Two additional identified CSIs are shared by members of the novel family-level taxon (f_HBI72195) comprising the proposed genera Guptibacillus and Exobacillus, for which we are proposing the name Guptibacillaceae fam. nov. Lastly, the results presented here also show that 'Pseudalkalibacillus hemicentroti' and 'Pseudalkalibacillus macyae' are later heterotypic synonyms of Guptibacillus hwajinpoensis. These changes, which reliably depict the evolutionary relationships among Pseudalkalibacillus species, should be helpful in future studies of these organisms.

Diverse spore-forming bacterial populations in US organic raw milk are driven by climate region

Spore-forming bacteria pose significant challenges to the dairy industry, as they are present at high levels in the natural environment and can cause finished product spoilage. To improve organic raw milk quality and minimize spoilage caused by spore-forming bacteria, we used a farm-to-table approach, by assessing the levels and diversity of various spore types through longitudinal studies of United States (US) organic dairy supplies, including (1) raw milk from 100 organic dairy farms, (2) raw milk intended for organic cheese production from 5 processing plants, (3) pasteurized milk from 5 processing plants, and (iv) dairy powders from 2 processing plants. Based on a total of 4,194 isolates characterized by either rpoB or 16S rRNA gene sequencing, Bacillus spp. dominated the aerobic spore-formers isolated from farm raw milk, pasteurized milk, and powders. Nonmetric multidimensional scaling revealed that aerobic spore-former populations in organic farm raw milk differ significantly between climate zones at genus, species, and allelic type levels. The anaerobic/facultative anaerobic spore-formers isolated from farm and cheese raw milk samples represented the orders Clostridiales and Bacillales. Evaluation of the gas produced by anaerobic/facultative anaerobic spore-forming bacteria isolates showed that gas production varied significantly between Clostridiales clades, and 1 Bacillales clade produced gas amounts that were not significantly different from most Clostridiales clades. Overall, our data indicate (1) a substantial diversity of aerobic and anaerobic spore-formers in US organic dairy supplies with predominant genera and species similar between organic and conventional dairy supplies as previously described; (2) both anaerobic and facultative anaerobic spore-formers found in organic raw milk produce gas; and (3) climate may affect aerobic spore-former diversity in farm raw milk.

Mixing of Two Microbial Consortia in the Search for Stimulating Chromium Depletion

Two bacterial consortia (C55 and C33), obtained from an industrial residue contaminated with hexavalent chromium (Cr(VI)), were used to study the behavior of their mixture for depleting this ion in liquid media. In the absence of Cr(VI), C55 showed a greater growth rate than C33, while the latter exhibited biofilm formation. In the presence of this ion, C55 showed resistance up to 800 mg·L-1 and an ability to diminish up to 400 mg·L-1 of the Cr(VI) from the medium, while for C33, these concentrations were 400 and 200 mg·L-1, respectively. Bacterial synergism between these consortia was evaluated using different compound ratios (C55:C33 ratios of 1:1, 1:2, and 2:1), growing at 50, 100, and 200 mg·L-1 Cr(VI). The best half-lives of Cr(VI) decrease were 16, 31, and 98 h, respectively, for the 1:1 mixture. The ability of C33 and the mixed consortia to form biofilms was verified. MiSeq sequencing revealed 4 major populations for C55 (in a total of 14) and 3 for C33 (8), most of which were common. After an isolation process, 2 bacterial strains were obtained from C55 and 4 from C33. Three of these strains (QRePLB33E, similar to Oceanobacillus profundus; QRePLB33G, to Shouchella clausii; and QRePLB55C, to Cellulosimicrobium funkei) showed resistance to Cr(VI) and the ability to remove 100% of it at least up to 300 mg·L-1. Thus, synergism between different bacterial consortia obtained from the same site is possible and can improve, by complementing their capacities, both the growth rate and the ability to diminish the xenobiotic from the medium.

Diving into freshwater microbial metabolites: Pioneering research and future prospects

In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.

An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022-2023

The description of new taxa and nomenclature updates to currently known taxa from aquatic animal species continues. After a review of the literature from 2022 and 2023, multiple lists of bacteria, including members of Phylum Planctomycetota, were compiled. As with the previous review, most bacteria are oxidase-positive Gram-negative bacilli with familiar families including new taxa in Aeromonadaceae, Flavobacteriaceae, and Vibrionaceae. A number of Gram-positive bacilli are described including new taxa in the Nocardioides, Paenibacillus, and Streptomyces genera. Two anaerobic species are listed, and one new member of Family Planctomycetaceae is noted. Revised taxa are briefly mentioned. The majority of new and revised taxa are isolated from healthy aquatic animals, and therefore, the role of these new bacteria in health and disease is unknown. Bacteria with pathogenic association and potential production of bioactive substances are highlighted.

Randomized Clinical Trials Demonstrate the Safety Assessment of Alkalihalobacillus clausii AO1125 for Use as a Probiotic in Humans

(1) Background: Alkalihalobacillus clausii AO1125 is a Gram-positive, motile, spore-forming bacterium with potential as a probiotic due to its broad-spectrum antimicrobial activity, inhibiting pathogens like Listeria monocytogenes, Staphylococcus aureus, and Clostridium difficile, as well as anti-rotavirus activity. Its resilience in gastrointestinal conditions suggests benefits for gut health. This study evaluates the safety and probiotic potential of A. clausii AO1125. (2) Methods: Genome annotation identified genes linked to probiotic traits such as stress resistance, gut colonization, immune modulation, and antimicrobial production. The genome was screened for antibiotic resistance genes using CARD, bacteriocin clusters using BAGEL4, and virulence factors via VFDB. Cytotoxicity was assessed on Vero cells and erythrocytes, and a Phase I, double-blind, placebo-controlled clinical trial was conducted with 99 healthy volunteers (50 AO1125, 49 placebo). (3) Results: Genomic analysis confirmed minimal antibiotic resistance genes and the absence of virulence factors, supporting safety. A. clausii AO1125 showed no pathogenicity, cytotoxicity, or hemolytic activity and was well-tolerated in clinical settings, with mild, transient abdominal gas as the most common adverse event. (4) Conclusions: The safety profile and genetic basis for probiotic and antimicrobial properties support A. clausii AO1125 as a promising probiotic candidate for gastrointestinal health, warranting further clinical research.

A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families

The order Caryophanales, belonging to class Bacilli, is globally distributed in various ecosystems. Currently, this order comprised 12 families that show vast phenotypic, ecological and genotypic variation. The classification of Caryophanales at the family level is currently mainly based on 16S rRNA gene sequencing analysis and the presence of shared phenotypic characteristics, resulting in noticeable anomalies. Our present study revises the taxonomy of Caryophanales based on 1080 available high-quality genome sequences of type strains. The evaluated parameters included the core-genome phylogeny, pairwise average aa identity, lineage-specific core genes, physiological criteria and ecological parameters. Based on the results of this polyphasic approach, we propose that the order Caryophanales be reclassified into 41 families, which include the existing 12 families, 17 families in a recent Validation List in the IJSEM (Validation List no. 215) and 12 novel families for which we propose the names Aureibacillaceae, Cytobacillaceae, Domibacillaceae, Falsibacillaceae, Heyndrickxiaceae, Lottiidibacillaceae, Oxalophagaceae, Pradoshiaceae, Rossellomoreaceae, Schinkiaceae, Sulfoacidibacillaceae and Sutcliffiellaceae. This work represents a genomic sequence-based and systematic framework for classifying the order Caryophanales at the family level, providing new insights into its evolution.

Comparative Genomics and In Vitro Experiments Provide Insight into the Adaptation and Probiotic Properties of Shouchella clausii

Shouchella clausii (S. clausii) has been marketed as an important commercial probiotic, displaying significant therapeutic effects on antibiotic-associated diarrhea and providing benefits to humans. This study aimed to explore the distribution, adaptation, and probiotic properties of S. clausii. Based on 16S rRNA gene analysis, 43 strains of S. clausii were isolated from 317 soil samples in China. Based on the genomic index of Average Nucleotide Identity (ANI) results, 41 strains were confirmed as S. clausii, while two strains, FJAT-45399 and FJAT-45335, were identified as potential novel species distinct from S. clausii. Combined phenotypic and genomic predictions indicated that S. clausii could survive under harsh conditions. Comparative genomics revealed that these isolates possess antibiotic resistance genes, as well as capabilities for bacteriocin and folate production, while lacking toxins and hemolytic activity. Hemolysis tests indicated that strain FJAT-41761 exhibited non-pathogenic γ-hemolytic activity, while also demonstrating resistance to multiple antibiotics, consistent with probiotic characteristics. These findings suggest that strain FJAT-41761 is safe and holds potential as a future probiotic.

Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans

An improved approach was developed for the genetic manipulation of the Gram-positive extremophile Halalkalibacterium halodurans (formerly called Bacillus halodurans). We describe an allelic replacement method originally developed for Staphylococcus aureus that allows the deletion, mutation, or insertion of genes without leaving markers or other genetic scars. In addition, a protocol for rapid in vitro plasmid methylation and transformation is presented. The combined methods allow the routine genetic manipulation of H. halodurans from initial transformation to the desired strain in 8 days. These methods improve H. halodurans as a model organism for the study of extremophiles.

Investigating Polyextremophilic Bacteria in Al Wahbah Crater, Saudi Arabia: A Terrestrial Model for Life on Saturn's Moon Enceladus

The study of extremophilic microorganisms has sparked interest in understanding extraterrestrial microbial life. Such organisms are fundamental for investigating life forms on Saturn's icy moons, such as Enceladus, which is characterized by potentially habitable saline and alkaline niches. Our study focused on the salt-alkaline soil of the Al Wahbah crater in Saudi Arabia, where we identified microorganisms that could be used as biological models to understand potential life on Enceladus. The search involved isolating 48 bacterial strains, sequencing the genomes of two thermo-haloalkaliphilic strains, and characterizing them for astrobiological application. A deeper understanding of the genetic composition and functional capabilities of the two novel strains of Halalkalibacterium halodurans provided valuable insights into their survival strategies and the presence of coding genes and pathways related to adaptations to environmental stressors. We also used mass spectrometry with a molecular network approach, highlighting various classes of molecules, such as phospholipids and nonproteinogenic amino acids, as potential biosignatures. These are essential features for understanding life's adaptability under extreme conditions and could be used as targets for biosignatures in upcoming missions exploring Enceladus' orbit. Furthermore, our study reinforces the need to look at new extreme environments on Earth that might contribute to the astrobiology field.

Two Novel Alkaliphilic Species Isolated from Saline-Alkali Soil in China: Halalkalibacter flavus sp. nov., and Halalkalibacter lacteus sp. nov

The degradation of farmland in China underscores the need for developing and utilizing saline-alkali soil. Soil health relies on microbial activity, which aids in the restoration of the land's ecosystem, and hence it is important to understand microbial diversity. In the present study, two Gram-stain-positive strains HR 1-10T and J-A-003T were isolated from saline-alkali soil. Preliminary analysis suggested that these strains could be a novel species. Therefore, the taxonomic positions of these strains were evaluated using polyphasic analysis. Phylogenetic and 16S rRNA gene sequence analysis indicated that these strains should be assigned to the genus Halalkalibacter. Cell wall contained meso-2,6-diaminopimelic acid. The polar lipids present in both strains were diphosphatidyl-glycerol, phosphatidylglycerol, and an unidentified phospholipid. The major fatty acids (>10%) were anteiso-C15:0, C16:0 and iso-C15:0. Average nucleotide identity and digital DNA#x2013;DNA hybridization values were below the threshold values (95% and 70%, respectively) for species delineation. Based on the above results, the strains represent two novel species of the genus Halalkalibacter, for which the names Halalkalibacter flavus sp. nov., and Halalkalibacter lacteus sp. nov., are proposed. The type strains are HR 1-10T (=GDMCC 1.2946T = MCCC 1K08312T = JCM 36285T), and J-A-003T (=GDMCC 1.2949T = MCCC 1K08417T = JCM 36286T).

POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy

SUMMARY

Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies.

AVAILABILITY AND IMPLEMENTATION

The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.

Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources

Ornate, large, extremophilic (OLE) RNAs comprise a class of large noncoding RNAs in bacteria whose members form a membrane-associated ribonucleoprotein (RNP) complex. This complex facilitates cellular adaptation to diverse stresses such as exposure to cold, short-chain alcohols, and elevated Mg2+ concentrations. Here, we report additional phenotypes exhibited by Halalkalibacterium halodurans (formerly called Bacillus halodurans) strains lacking functional OLE RNP complexes. Genetic disruption of the complex causes restricted growth compared to wild-type cells when cultured in minimal media (MM) wherein glucose is replaced with alternative carbon/energy sources. Genetic suppressor selections conducted in glutamate MM yielded isolates that carry mutations in or near genes relevant to Mn2+ homeostasis (ykoY and mntB), phosphate homeostasis (phoR), and putative multidrug resistance (bmrCD). These functional links between OLE RNA, carbon/energy management, and other fundamental processes including protein secretion are consistent with the hypothesis that the OLE RNP complex is a major contributor to cellular adaptation to unfavorable growth conditions.

Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater

The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.

Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022

Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.

Two novel alkalitolerant species Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov

In this study, two novel alkalitolerant strains (FJAT-53046T and FJAT-53715T) were isolated from sediment samples collected in Zhangzhou, PR China. Phylogeny based on 16S rRNA gene sequences suggested that strains FJAT-53046T and FJAT-53715T were new members of the genus Pseudalkalibacillus. The two novel strains showed the highest 16S rRNA gene sequence similarity to Pseudalkalibacillus hwajinpoensis DSM 16206T, with values of 97.4 and 97.6 %, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and the reference strain were 77.2 and 79.6 %, 20.9 and 30.2 %, respectively, which were below the prokaryotic species delineation thresholds. The ANI and dDDH values between strains FJAT-53046T and FJAT-53715T were 86.0 and 30.2 %, respectively, suggesting that they belonged to different species in the genus Pseudalkalibacillus. The major respiratory quinone in both strains was MK-7 and the major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids in both novel strains. Combined with results stemming from the determination of physical and biochemical characteristics, chemical properties, and genome analysis, strains FJAT-53046T and FJAT-53715T are proposed to represent two novel species of the genus Pseudalkalibacillus, for which the names Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov. are proposed. The type strains are FJAT-53046T (=GDMCC 1.3077T=JCM 35611T) and FJAT-53715T (=GDMCC 1.3076T=JCM 35610T), respectively.

Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.

Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants

The "universal target" region of the gene encoding the 60 kDa chaperonin protein (cpn60, also known as groEL or hsp60) is a proven sequence barcode for bacteria and a useful target for marker gene amplicon-based studies of complex microbial communities. To date, identification of cpn60 sequence variants from microbiome studies has been accomplished by alignment of queries to a reference database. Naïve Bayesian classifiers offer an alternative identification method that provides variable rank classification and shorter analysis times. We curated a set of cpn60 barcode sequences to train the RDP classifier and tested its performance on data from previous human microbiome studies. Results showed that sequences accounting for 79%, 86% and 92% of the observations (read counts) in saliva, vagina and infant stool microbiome data sets were classified to the species rank. We also trained the QIIME 2 q2-feature-classifier on cpn60 sequence data and demonstrated that it gives results consistent with the standalone RDP classifier. Successful implementation of a naïve Bayesian classifier for cpn60 sequences will facilitate future microbiome studies and open opportunities to integrate cpn60 amplicon sequence identification into existing analysis pipelines.

Alkalihalobacillus deserti sp. nov., Isolated from the Saline-Alkaline Soil

A bacterial strain, designated TRPH29^T, was isolated from saline-alkaline soil, collected from the southern edge of the Gurbantunggut desert, Xinjiang, People's Republic of China. The isolate was Gram-staining positive, facultatively anaerobic, straight rods. Growth occurred at 15-40 °C (optimum, 28 °C), pH 8.0-13.0 (optimum, 10.0), and in the presence of 0-15% (w/v) NaCl (optimum, 2%). Phylogenetic analysis using 16S rRNA gene sequence indicated that strain TRPH29^T showed the highest sequence similarities to Alkalihalobacillus krulwichiae (98.31%), Alkalihalobacillus wakoensis (98.04%), and Alkalihalobacillus akibai (97.69%). Average nucleotide identity (ANI) and digital DNA-DNA hybridization values between strain TRPH29^T and Alkalihalobacillus krulwichiae, Alkalihalobacillus wakoensis, Alkalihalobacillus akibai were in the range of 73.62-75.52% and 15.0-21.20%, respectively. Results of genome analyses indicated that the genome size of strain TRPH29^T was 5.05 Mb, with a genomic DNA G + C content of 37.30%. Analysis of the cellular component of strain TRPH29^T revealed that the primary fatty acids were anteiso-C_15:0 and iso-C_15:0, and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid, and an unidentified phospholipid. The predominant respiratory quinone was MK-7. Based on the genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain TRPH29^T represents a novel species of the genus Alkalihalobacillus, for which the name Alkalihalobacillus deserti sp. nov. is proposed. The type strain is TRPH29^T (= CGMCC 1.19067^T = NBRC 115475^T).

A Microbiological Approach to Alleviate Soil Replant Syndrome in Peaches

Replant syndrome (RS) is a global problem characterized by reduced growth, production life, and yields of tree fruit/nut orchards. RS etiology is unclear, but repeated monoculture plantings are thought to develop a pathogenic soil microbiome. This study aimed to evaluate a biological approach that could reduce RS in peach (Prunus persica) orchards by developing a healthy soil bacteriome. Soil disinfection via autoclave followed by cover cropping and cover crop incorporation was found to distinctly alter the peach soil bacteriome but did not affect the RS etiology of RS-susceptible 'Lovell' peach seedlings. In contrast, non-autoclaved soil followed by cover cropping and incorporation altered the soil bacteriome to a lesser degree than autoclaving but induced significant peach growth. Non-autoclaved and autoclaved soil bacteriomes were compared to highlight bacterial taxa promoted by soil disinfection prior to growing peaches. Differential abundance shows a loss of potentially beneficial bacteria due to soil disinfection. The treatment with the highest peach biomass was non-autoclaved soil with a cover crop history of alfalfa, corn, and tomato. Beneficial bacterial species that were cultivated exclusively in the peach rhizosphere of non-autoclaved soils with a cover crop history were Paenibacillus castaneae and Bellilinea caldifistulae. In summary, the non-autoclaved soils show continuous enhancement of beneficial bacteria at each cropping phase, culminating in an enriched rhizosphere which may help alleviate RS in peaches.

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.

Shouchella tritolerans sp. nov., a facultative anaerobic bacterium isolated from marine sediments

An alkali, salt, and thermo-tolerant strain designated FJAT-45399^T was isolated from marine sediment in Fujian Province, China. Strain FJAT-45399^T was Gram-stain-positive, rod-shaped, and facultatively aerobic. It shared high 16S rRNA gene sequence similarities with the members of the genus Shouchella. Further, the phylogenetic and phylogenomic analysis also suggested strain FJAT-45399^T clustered with the members of the genus Shouchella. Growth of strain FJAT-45399^T was observed at 15-55 °C (optimum 45-50 °C), pH 7.0-13.0 (optimum 9.0) and 0-15% (w/v) NaCl (optimum 2%). It contained MK-7 as the menaquinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and an unidentified glycolipid (UGL) and lipid (UL). The major fatty acids (> 10%) were C_16:0 (22.8%), iso-C_15:0 (21.3%), and anteiso-C_15:0 (14.0%). The genomic DNA G + C content was 44.5%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain FJAT-45399^T and the most closely related type strain Shouchella clausii DSM 8716^T (ANI 94.1% and dDDH 55.4%) were both below the cut-off level for species delineation. Based on the above results, strain FJAT-45399^T represents a novel species of the genus Shouchella, for which the name Shouchella tritolerans sp. nov., is proposed. The type strain is FJAT-45399^T (= GDMCC 1.3098^T = JCM 35613^T).

Genomic insights of an alkaliphilic bacterium Halalkalibacter alkaliphilus sp. nov. isolated from an Indian Soda Lake

An alkaliphilic, Gram-stain-positive, non-motile, rod-shaped, and spore forming bacterial strain (MEB205^T) was isolated from sediment sample collected from Lonar lake, India. The strain grew optimally at pH 10, NaCl concentration of 3.0% at 37 °C. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain MEB205^T belonged to the genus Halalkalibacter in the family Bacillaceae and shared the highest sequence similarity with H. okhensis Kh10-101^T (98.9%) followed by H. wakoensis N-1 ^T (98.7%). The assembled genome of strain MEB205^T has a total length of 4.8 Mb with a G + C content of 37.8%. The dDDH and OrthoANI values between strain MEB205^T and H. okhensis Kh10-101 ^T were 29.1% and 84.3%, respectively. Furthermore, the genome analysis revealed the presence of antiporter genes (nhaA and nhaD) and L-ectoine biosynthesis gene required for survival of the strain MEB205^T in alkaline-saline habitat. The major fatty acid was C_15:0 anteiso, C_16:0 and C_15:0 iso (> 10.0%). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. meso-diaminopimelic acid was diagnostic diamino acid for cell wall peptidoglycan. Based on the polyphasic taxonomic studies, strain MEB205^T represent a novel species of the genus Halalkalibacter for which the name Halalkalibacter alkaliphilus sp. nov. (Type strain MEB205^T = MCC 3863 ^T = JCM 34004 ^T = NCIMB 15406 ^T) is proposed.

Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

Temperature drives the assembly of Bacillus community in mangrove ecosystem

Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO₃-N and NH₄-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.

Pseudalkalibacillus salsuginis sp. nov., a novel salt-tolerant bacterium isolated from a saline lake sediment

A salt-tolerant bacterium, designated strain EGI L200015T, was isolated from saline lake sediment in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that EGI L200015T formed a distinct clade with Pseudalkalibacillus berkeleyi KCTC 12718T with sequence identity of 98.3%. The novel isolate could be distinguished from species of the genus Pseudalkalibacillus by its distinct phenotypic, physiological and genotypic characteristics. Cells of EGI L200015T were aerobic, Gram-stain-positive, non-motile and rod-shaped. Optimal growth conditions for EGI L200015T occurred on marine agar 2216 at pH 8.0 at 30 °C. The major respiratory quinone was MK-7, while the major fatty acids (> 10 %) were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The detected polar lipids of included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the genome sequence data, the DNA G+C content of EGI L200015T was 41.6 %. On the basis of the phenotypic, physiological, genotypic and phylogenetic data, strain EGI L200015T represents a novel species of the genus Pseudalkalibacillus , for which the name Pseudalkalibacillus salsuginis sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200015T (= KCTC 43363T = CGMCC 1.19260T).

Parachryseolinea silvisoli gen. nov., sp. nov., isolated from forest soil, and reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov

A lemon-chiffon strain, designated QH1ED-6-2^T, was isolated from a soil sample collected from Qinghai Virgin Forests, Qinghai Province, PR China. The strain was Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain QH1ED-6-2^T belongs to the family Fulvivirgaceae, and has the highest similarity values of 93.6-92.0 % to Ohtaekwangia koreensis CCUG 58939^T, Ohtaekwangia kribbensis CCUG 58938^T, Chryseolinea flava SDU1-6^T and Chryseolinea serpens DSM 24574^T, respectively. The major cellular fatty acids included iso-C_15 : 0, C_16 : 1  ω5c, iso-C_17 : 0 3-OH and summed feature 3. The major polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone-7. The average amino acid identity values and percentages of conserved proteins between QH1ED-6-2^T and its closely related genera were 66.4-69.6 % and 58.9-64.9 %, respectively, which are interspersed in the intra-genera cutoff values. The digital DNA-DNA hybridization values were 17.6-19.2 %. The draft genome size of strain QH1ED-6-2^T was 7.98 Mbp with a DNA G+C content of 51.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic data, genomic DNA G+C content, as well as AAI, POCP and dDDH results, strain QH1ED-6-2^T represents a novel species of a new genus in the family Fulvivirgaceae, for which the name Parachryseolinea silvisoli sp. nov. is proposed. The type strain is QH1ED-6-2^T (=GDMCC 1.2318^T=JCM 35041^T). We also propose the reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov. (type strain SDU1-6^T=CGMCC 1.13492^T=JCM 32520^T).

Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins from Bacillaceae

The subtilase family (S8), a member of the clan SB of serine proteases are ubiquitous in all kingdoms of life and fulfil different physiological functions. Subtilases are divided in several groups and especially subtilisins are of interest as they are used in various industrial sectors. Therefore, we searched for new subtilisin sequences of the family Bacillaceae using a data mining approach. The obtained 1,400 sequences were phylogenetically classified in the context of the subtilase family. This required an updated comprehensive overview of the different groups within this family. To fill this gap, we conducted a phylogenetic survey of the S8 family with characterised holotypes derived from the MEROPS database. The analysis revealed the presence of eight previously uncharacterised groups and 13 subgroups within the S8 family. The sequences that emerged from the data mining with the set filter parameters were mainly assigned to the subtilisin subgroups of true subtilisins, high-alkaline subtilisins, and phylogenetically intermediate subtilisins and represent an excellent source for new subtilisin candidates.

In vitro evaluation of antiviral activity of Shouchella clausii probiotic strain and bacterial supernatant against herpes simplex virus type 1

Herpes simplex virus-1 (HSV-1) is an important human neurotropic virus infecting 70% of the world population. Due to the emergence of viral resistance via mutations in HSV-1 genes and some of the adverse effects of antiviral compounds, there is a growing need for safe, novel, and effective therapeutic and preventive strategies. The aim of the present study was to investigate for the first time the potential antiviral activity of Shouchella clausii probiotic strain and bacterial supernatant against HSV-1. The MTT assay was used to determine the possible cytotoxicity of the S. clausii and bacterial supernatant. Vero cells were treated by S. clausii, bacterial supernatant, and HSV-1 under pre-treatment (incubation of Vero cells with S. clausii then HSV-1 inoculation), pre-incubation (mixture of co-incubated HSV-1/S. clausii added to Vero cell), competition (adding HSV-1 and S. clausii into Vero cells simultaneously) and post-treatment (Vero cells inoculated with HSV-1 then incubated with S. clausii) assays. Viral titer reduction (TCID₅₀) and viral DNA relative quantification by real-time PCR were measured in each experimental condition. The results indicated that S. clausii and its supernatant had the greatest inhibitory activity toward HSV-1 in pre-treatment assay. The HSV-1 titer treated with S. clausii, and bacterial supernatant was 3.6 and 2.2 Log₁₀TCID₅₀/mL lower compared to the control (7.66 Log₁₀TCID₅₀/mL). Results showed an antiviral effect of S. clausii and its supernatant. S. clausii could be considered as a novel inhibitor for HSV-1 infection.