Bacillus camelliae sp. nov., isolated from Pu'er tea

Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods

Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods.

Genome-based reclassification of Bacillus acidicola, Bacillus pervagus and the genera Heyndrickxia, Margalitia and Weizmannia

In the present study, the taxonomic positions of Bacillus acidicola, Bacillus pervagus and members of the genera Heyndrickxia, Margalitia and Weizmannia were evaluated. The 16S rRNA gene sequence similarity between Bacillus acidicola DSM 14745^T, Bacillus pervagus DSM 23947^T and members of the genera Heyndrickxia and Margalitia were above the cut-off level (>95 %) for genus delineation. Amino acid identity (AAI) values and the results of phylogenomic analysis suggested that B. acidicola and the members of the genera Heyndrickxia, Margalitia and Weizmannia belong to the same genus. Furthermore, the AAI and phylogenomic results also differentiate B. pervagus from B. acidicola and the members of the genera Heyndrickxia, Margalitia and Weizmannia. Based on the results, we propose to transfer Bacillus acidicola, Margalitia and Weizmannia to the genus Heyndrickxia. We also propose the reclassification of B. pervagus into a new genus Oikeobacillus gen. nov., with the type species Oikeobacillus pervagus comb. nov.

Stappia sediminis sp. nov., isolated from rhizosphere soil of coastal herb Zoysia matrella within the Beibu Gulf

A bacterial isolate (BGMRC 2046^T) was isolated from the rhizosphere soil of Zoysia matrella collected from the Beibu Gulf of China. The results of a polyphasic taxonomic study revealed that this strain belongs to a member of the genus Stappia with the characteristics of Gram-stain-negative, catalase- and oxidase-positive, motile, short rod-shaped. The strain grew at 20-37 °C (optimal, 28 °C), pH 6.0-9.0 (optimal, pH 7.0), and 1-7% (w/v) optimal, NaCl (1-3%). A phylogenetic evaluation based on 16S rRNA gene sequence analysis revealed that this strain fall into the family Stappiaceae, being most closely related to Stappia indica CGMCC 1A01226^T (95.8% sequence similarity), Stappia stellulata DSM 5886^T (95.1%), and Stappia taiwanensis DSM 23284^T (94.4%). The major cellular fatty acid, respiratory quinone and polar lipids were all detected from new species (BGMRC 2046T), that shows the chemical characteristics of BGMRC 2046T. The major polar lipids were two unidentified ninhydrin positive phospholipids, four unidentified phospholipids, and one unidentified lipid. Genome sequencing revealed a genome size of 4.78 Mbp and a G + C content of 60.8%. Pairwise comparison of the genomes of the new strain BGMRC 2046^T and the three most closely related strains resulted in gANI values was lower than 75% and a digital DNA-DNA hybridization values was lower than 24%. The strain possessed genes encoding choline uptake and conversion to betaine gene clusters. The results of the polyphasic taxonomic study showed that strain BGMRC 2046^T represents a new species of the genus Stappia. The name Stappia sediminis sp. nov. is proposed for the species with the type strain BGMRC 2046^T (= KCTC52115^T = CGMCC1.17425^T).

Pararhizobium mangrovi sp. nov., Isolated From Aegiceras corniculatum Stem

A novel Gram-stain-negative, catalase- and oxidase-positive, motile, short rod-shaped bacterium designated BGMRC 6574^T was isolated from stems of Aegiceras corniculatum collected from Hainan province, China. The strain grew at 25-37 °C (optimal at 28 °C), pH 5.0-10.0 (pH 7.0), and 3-8% (w/v) NaCl (3%). Based on the 16S rRNA phylogenetic analysis, the strain was closely related to Pararhizobium haloflavum MCCC 1K03228^T (96.45% sequence similarity). The novel strain showed an average nucleotide identity value and a digital DNA-DNA hybridization of 72.62 and 27.1%, respectively, to P. haloflavum MCCC 1K03228^T based on draft genome sequences. The G+C content of the genomic DNA was 64.7 mol%. The major respiratory quinone was Q-10. The strain possessed genes putatively encoding choline uptake and conversion to betaine gene clusters. The extract significantly delayed the lifespan of Caenorhabditis elegans compared to the control (P < 0.05). The major polar lipids were phosphatidylcholine, seven unidentified phospholipids, three unidentified ninhydrin-positive phospholipids, and two unidentified lipids. The major cellular fatty acid was C_19:0 cyclo ω8c. The results of a polyphasic taxonomic study showed that strain BGMRC 6574^T represents a new species of the genus Pararhizobium, and it was named Pararhizobium mangrovi sp. nov. The type strain is BGMRC 6574^T (=KCTC 72636^T = CGMCC 1.16783).

Martelella alba sp. nov., isolated from mangrove rhizosphere soil within the Beibu Gulf

Strain BGMRC 2036^T was isolated from rhizosphere soil of Bruguiear gymnorrhiza collected from the Beibu Gulf of China. Optimum growth occurred at 28 °C, pH 7.0, and under the conditions of 3-5% (w/v) NaCl. The phylogenetic comparisons of 16S rRNA gene sequences displayed that strain BGMRC 2036^T was closely related to Martelella limonii NBRC109441^T (96.6% sequence similarity), M. mediterranea CGMCC 1.12224^T (96.5%), M. lutilitoris GH2-6^T (96.5%), M. radicis BM5-7^T (96.2%), and M. mangrove BM9-1^T (95.9%), M. suaedae NBRC109440^T (95.8%). The phylogenomic tree based on the up-to-date bacterial core gene set indicated that the strain BGMRC 2036^T form a clade formed with members of the genera Martelella. The major polar lipids include phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphotidylinositol, two unidentified phospholipids, and three unidentified ninhydrin positive phospholipids. The major respiratory quinone is Q-10, which is similar to those of genera Martelella. The main cellular fatty acids are C_18:1 ω7c, C_16:0, and C_12:0 aldehyde. Genome sequencing revealed a genome size of 4.99 Mbp and a G + C content of 62.3 mol%. Pairwise comparison of the genomes of the new strain BGMRC 2036^T and the three reference strains M. endophytica YC 6887^T, M. mediterranea CGMCC 1.12224^T, and M. mangrovi USBA-857 indicated that gANI value was lower than 81% and a digital DNA-DNA hybridization value was lower than 27%. The strain BGMRC 2036^T possessed genes putatively encoding riboflavin synthesis and flavodoxin A polyphasic taxonomic study suggested that strain BGMRC 2036^T represented a novel species belonging to the genus Martelella, and it was named Martelella alba sp. nov. The type strain is BGMRC 2036^T (=KCTC 52121^T =NBRC 111908^T).

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

Falsibacillus albus sp. nov., isolated from mangrove soil

A novel Gram-stain-positive, catalase- and oxidase-positive, endospore-forming bacterium, designated GY 10110^T, was isolated from mangrove soil collected from Qinzhou, Guangxi province, China. Cells were aerobic, motile with peritrichous flagella and rod-shaped. The strain grew at 15-37 °C (optimum, 28 °C), at 0-3 %(w/v) NaCl (1 %) and at pH 6.0-9.0 (pH 7.0). The major fatty acids of strain GY 10110^T were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, glycolipid, two unidentified aminophospholipids and three unidentified phospholipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GY 10110^T was closely related to Falsibacillus pallidus CCTCC AB 207188^T (98.0 % sequence similarity) and Bacillus oceanisediminis CGMCC 1.10115^T (96.9 %), respectively. The G+C content of strain GY 10110^T based on the whole genome sequence was 42.3 mol%. The novel strain showed an average nucleotide identity (ANI) value of 77.8 % and a digital DNA-DNA hybridization (dDDH) value of 15.6 % with Falsibacillus pallidus CCTCC AB 207188^T based on draft genome sequences, followed by Bacillus oceanisediminis CGMCC 1.10115^T with ANI and dDDH values of 75.2 and 12.8 %, respectively. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analysis, showed that strain GY 10110^T represents a novel species of the genus Falsibacillus, for which the name Falsibacillus albus sp. nov. is proposed. The type strain is GY 10110^T (=CGMCC 1.13648^T=NBRC 113502^T).

Genomic and metabolic features of the Bacillus amyloliquefaciens group- B. amyloliquefaciens, B. velezensis, and B. siamensis- revealed by pan-genome analysis

The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B. amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan-genome analysis combined with an experimental verification of some of the functions identified. All B. amyloliquefaciens group genomes were retrieved from GenBank and their phylogenetic relatedness was subsequently investigated. Genome comparisons of B. amyloliquefaciens, B. siamensis, and B. velezensis showed that their genomic and metabolic features were similar; however species-specific features were also identified. Energy metabolism-related genes are more enriched in B. amyloliquefaciens, whereas secondary metabolite biosynthesis-related genes are enriched in B. velezensis. Compared to B. amyloliquefaciens and B. siamensis, B. velezensis harbors more genes in its core-genome which are involved in the biosynthesis of antimicrobial compounds, as well as genes involved in d-galacturonate and d-fructuronate metabolism. B. amyloliquefaciens, B. siamensis, and B. velezensis all harbor a xanthine oxidase gene cluster (xoABCDE) in their core-genomes that is involved in metabolizing xanthine and uric acid to glycine and oxalureate. A reconstruction of B. amyloliquefaciens group metabolic pathways using their individual pan-genomes revealed that the B. amyloliquefaciens group strains have the ability to metabolize diverse carbon sources aerobically, or anaerobically, and can produce various metabolites such as lactate, ethanol, acetate, CO₂, xylitol, diacetyl, acetoin, and 2,3-butanediol. This study therefore provides insights into the genomic and metabolic features of the B. amyloliquefaciens group.