Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

Brucella microti and Rodent-Borne Brucellosis: A Neglected Public Health Threat

Brucellosis is one of the most important zoonoses worldwide, primarily affecting livestock but also posing a serious threat to public health. The major Brucella species are known to cause a feverish disease in humans with various clinical signs. These classical Brucella species are (re-)emerging, but also novel strains and species, some of them transmitted from rodents, can be associated with human infections. As a result of our review on rodent-borne brucellosis, we emphasise the need for more comprehensive surveillance of Brucella and especially Brucella microti in rodent populations and call for further research targeting the ecological persistence of rodent-associated Brucella species in the environment, their epizootic role in wild rodents and their virulence and pathogenicity for wildlife.

Brucella anthropi bacteremia: persistent bacteremia with minimal symptoms

Brucella anthropi, an aerobic, glucose-nonfermenting gram-negative rod, is predominantly an opportunistic pathogen affecting immunosuppressed patients. This case report describes a 27-year-old woman with systemic lupus erythematosus who developed persistent B. anthropi bacteremia following a pregnancy termination. Despite her stable condition and minimal symptoms, including transient fever, blood cultures revealed persistent bacteremia. Initial treatment with ceftazidime was ineffective due to resistance, leading to a switch to ciprofloxacin, which ultimately resolved the bacteremia. This case underscores the challenges in identifying the source of infection in the absence of typical symptoms and highlights the importance of vigilance in monitoring for persistent bacteremia, even in clinically stable patients. Our findings suggest that symptom improvement does not guarantee the resolution of bacteremia, propose follow-up blood cultures to ensure effective management of B. anthropi bacteremia.

Facivitalis istanbulensis gen. nov., sp. nov., a novel member of the family Sphingomonadaceae with the potential for aromatic-degradation isolated from Jet A1 fuel

A novel gram-stain-indeterminate, rod-shaped, endospore-forming, motile, aerobic bacterium, designated JETA1-E2T, was isolated from aircraft fuel Jet A1 sample. The strain showed high pairwise similarity values of partial 16S rRNA gene sequences to Sphingomonas paucimobilis (MT367853) (99.42%), Sphingomonas sanguinis (MF319771) (99.34%), and Sphingomonas pseudosanguinis (HE716953) (99.27%) within the family Sphingomonadaceae. However, API test results revealed that the strain JETA1-E2T differed from these type strains. The phylogenetic tree based on the whole genome and the phylogenomic tree generated with the UBCG tool showed that the strain JETA1-E2T formed a distinct monophyletic clade within the family Sphingomonadaceae, and clustered distantly with the genera Sphingomonas and Sphingobium. The predominant respiratory quinone is Q-10. The major fatty acids are C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c). C19:0 is present in small amounts. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, aminophospholipid, unidentified glycolipid, and two unidentified sphingoglycolipids. The only polyamine is putrescine in minor amounts. The DNA G + C content of the type strain is 66.5 mol%. Several unique genes in the strain JETA1-E2T may contribute to fight against various stressors, virulence and pathogenicity, as well as survival in challenging conditions. The strain JETA1-E2T contains 100 of the characterised proteins available in the HADEG database of which 58% of these are involved in metabolic process of aromatics degradation. The findings indicate that the strain JETA1-E2T has the potential to metabolise hydrocarbons such as fuel, especially aromatic compounds. Based on the results of polyphasic taxonomic analyses, the strain JETA1-E2T represents a novel species in a new genus in the family Sphingomonadaceae for which the name Facivitalis istanbulensis gen. nov., sp. nov. is proposed. The type strain of Facivitalis istanbulensis is JETA1-E2T (DSM 117971T = LMG 33634T = KUEN 1206 (B) F3-1-1T).

Draft genomes of two Roseibium spp. isolated from the coral Pachyseris speciosa from a Singaporean reef

Two Roseibium spp. strains were isolated from skeletal macerates of the Singaporean coral Pachyseris speciosa at an ambient high temperature. We sequenced the genomes of SCP14 (JBDZYH000000000) and SCP15 (JBDZYI000000000), which revealed genomes containing genetic elements that play a role in coral health during thermal stress.

YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction

Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.

Extensive genomic study characterizing three Paracoccaceae populations and revealing Pseudogemmobacter lacusdianii sp. nov. and Paracoccus broussonetiae sp. nov

Bacteria within the family Paracoccaceae show promising potential for applications in various fields, garnering significant research attention. Three Gram stain-negative bacteria, strains CPCC 101601T, CPCC 101403T, and CPCC 100767, were isolated from diverse environments: freshwater, rhizosphere soil of Broussonetia papyrifera, and the phycosphere, respectively. Analysis of their 16S rRNA gene sequences, compared with those in the GenBank database, indicated that they belong to the family Paracoccaceae, with nucleotide similarities of 92.5%-99.9% to all of the Paracoccaceae members with valid taxonomic names. Phylogenetic studies based on 16S rRNA gene and whole-genome sequences identified CPCC 101601T as a member of the genus Pseudogemmobacter, CPCC 101403T belonging to the genus Paracoccus, and CPCC 100767 as part of the genus Gemmobacter. Notably, genomic analysis using average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; <70%) with their closely related strains suggested that CPCC 101601T and CPCC 101403T represent new species within their respective genera. Conversely, CPCC 100767 exhibited high ANI (98.5%) and dDDH (87.4%) values with Gemmobacter fulvus con5T, indicating it belongs to this already recognized species. The in-depth genomic analysis revealed that strains CPCC 101601T, CPCC 101403T, and CPCC 100767 harbor key genes related to the pathways for denitrifying, MA utilization, and polyhydroxyalkanoate biosynthesis. Moreover, genotyping and phenotyping analysis confirmed that strain CPCC 100767 has the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid, whereas CPCC 101601T can only perform the former bioprocess.IMPORTANCEBased on polyphasic taxonomic study, two new species, Pseudogemmobacter lacusdianii and Paracoccus broussonetiae, affiliated with the family Paracoccaceae were identified. This expands our understanding of the family Paracoccaceae and provides new microbial materials for further studies. Modern genomic techniques such as average nucleotide identity and digital DNA-DNA hybridization were utilized to determine species affiliations. These methods offer more precise results than traditional classification mainly based on 16S rRNA gene analysis. Beyond classification of these strains, the research delved into their genomes and discovered key genes related to denitrification, MA utilization, and polyhydroxyalkanoate biosynthesis. The identification of these genes provides a molecular basis for understanding the environmental roles of these strains. Particularly, strain CPCC 100767 demonstrated the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid. These bioprocess capabilities are of significant practical value, such as in agricultural production for use as biofertilizers or biostimulants.

Aurantiacibacter flavus sp. nov. and Aurantiacibacter gilvus sp. nov., isolated from the mudflat of Suaeda japonica colonies

Two novel strains were isolated from the mudflat of Suaeda japonica colonies in Incheon, Republic of Korea. Designated as DGU5T and DGU6T, these strains were Gram-stain-negative, facultatively anaerobic and rod-shaped and had yellowish colonies. Both strains were determined to belong to the genus Aurantiacibacter through phylogenetic analysis of their 16S rRNA sequences and draft genomes. The cells of strain DGU5T were non-motile and grew at temperatures ranging between 7-45°C (optimum, 25-30°C), pH 6.0-10.0 (optimum, 7.0-8.0) and in the presence of 0-11.0% NaCl (optimum, 2.0%). The cells of strain DGU6T were non-motile and grew in temperatures ranging from 10-45 °C (optimum, 30-35°C), pH 3.0-10.0 (optimum, 7.0-8.0) and in the presence of 0-11.0% NaCl (optimum, 2.0%). Overall genome relatedness index calculations revealed average nucleotide identity values (72.3-88.6%) and digital DNA-DNA hybridization values (18.8-35.9%) aligning with those of the genus Aurantiacibacter. The major fatty acids in both strains were C17:1 ω6c and summed feature 8 (C18:1 ω6c/C18:1 ω7c), while the predominant polar lipids were sphingoglycolipid, phosphatidylglycerol, and diphosphatidylglycerol. Phylogenetic, average nucleotide identity, digital DNA-DNA hybridization, physiological, and biochemical data collectively demonstrated the distinctiveness of the novel strains from other members within the family Erythrobacteraceae. We propose the names A. flavus sp. nov. (type strain DGU5T = KACC 23720T = TBRC 19015T) and A. gilvus sp. nov. (type strain DGU6T = KACC 23721T = TBRC 19016T) for the two strains.

Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral

The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989T, was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379T (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084T (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C18 : 1  ω7c and/or C18 : 1  ω6c and C16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989T and the type strains of P. litoris DSM 22379T and A. ishigakiensis ATCC BAA-2084T were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989T represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.

Options and considerations for validation of prokaryotic names under the SeqCode

Stable taxon names for Bacteria and Archaea are essential for capturing and documenting prokaryotic diversity. They are also crucial for scientific communication, effective accumulation of biological data related to the taxon names and for developing a comprehensive understanding of prokaryotic evolution. However, after more than a hundred years, taxonomists have succeeded in valid publication of only around 30 000 species names, based mostly on pure cultures under the International Code of Nomenclature of Prokaryotes (ICNP), out of the millions estimated to reside in the biosphere. The vast majority of prokaryotic species have not been cultured and are becoming increasingly known to us via culture-independent sequence-based approaches. Until recently, such taxa could only be addressed nomenclaturally via provisional names such as Candidatus or alphanumeric identifiers. Here, we present options and considerations to facilitate validation of names for these taxa using the recently established Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Community engagement and participation of relevant taxon specialists are critical and encouraged for the success of endeavours to formally name the uncultured majority.

Phylogenomic analyses of the Listeriaceae family support species reclassification and proposal of a new family and new genera

The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72-73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.

Hohaiivirga grylli gen. nov., sp. nov., a New Member of the Family Methylobacteriaceae, Isolated from Cricket (Gryllus chinensis)

A Gram-staining negative, non-motile, rod-shaped, oxidase negative and catalase positive strain WL0021T was isolated from cricket (Gryllus chinensis) living in the campus of Hohai University. Strain WL0021T was characterized utilizing a polyphasic taxonomy approach. The major fatty acids (> 5%) for strain WL0021T were C16:0 and summed feature 8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipid, two aminolipids, and an unidentified polar lipid. Ubiquinone-10 was detected as the predominant respiratory quinone. The results of 16S rRNA gene phylogenetic analyses revealed that strain WL0021T had the highest sequence similarity of 95.3% to Microvirga flavescens c27j1T and strain WL0021T formed a distinct linage within the family Methylobacteriaceae in the phylogenetic trees. Whole genomic DNA G+C content was 48.3%. Combined with the results from this study, strain WL0021T should represent a novel genus in the family Methylobacteriaceae, for which the name Hohaiivirga grylli gen. nov., sp. nov. (type strain WL0021T=GDMCC 1.2420T =JCM 34655T=MCCC 1K05886T) is proposed.

Comparative Study of Spectral and Functional Properties of Wild Type and Double Mutant H(L173)L/I(L177)H Reaction Centers of the Purple Bacterium Cereibacter sphaeroides

Previously, we found that in the reaction center (RC) of the purple bacterium Cereibacter sphaeroides, formation of heterodimeric primary electron donor (P) caused by the substitution of His-L173 by Leu, was compensated by the second mutation Ile-L177 - His. Significant changes in the spectral properties, pigment composition, and redox potential of P observed in the H(L173)L RC, are restored to the corresponding characteristics of the native RC in the RC H(L173)L/I(L177)H, with the difference that the energy of the long-wavelength QY optical transition of P increases significantly (by ~75 meV). In this work, it was shown using light-induced difference FTIR spectroscopy that the homodimeric structure of P is preserved in the RC with double mutation with partially altered electronic properties: electronic coupling in the radical-cation of the P+ dimer is weakened and localization of the positive charge on one of its halves is increased. Results of the study of the triple mutant RC, H(L173)L/I(L177)H/F(M197)H, are consistent with the assumption that the observed changes in the P+ electronic structure, as well as considerable blue shift of the QY P absorption band in the RC H(L173)L/I(L177)H, are associated with modification of the spatial position and/or geometry of P. Using femtosecond transient absorption spectroscopy, it was shown that the mutant H(L173)L/I(L177)H RC retains a sequence of reactions P* → P+BA- → P+HA- → P+QA- with electron transfer rates and the quantum yield of the final state P+QA- close to those observed in the wild-type RC (P* is the singlet-excited state of P; BA, HA, and QA are molecules of bacteriochlorophyll, bacteriopheophytin, and ubiquinone in the active A-branch of cofactors, respectively). The obtained results, together with the previously published data for the RC with symmetrical double mutation H(M202)L/I(M206)H, demonstrate that by introducing additional point amino acid substitutions, photochemical activity of the isolated RC from C. sphaeroides could be maintained at a high level even in the absence of important structural elements - axial histidine ligands of the primary electron donor P.

Sabulicella glaciei sp. nov., Isolated from Glacier, and Reclassification of Roseomonas rubea, Roseomonas ponticola and Roseomonas oleicola as Neoroseomonas rubea comb. nov., Falsiroseomonas ponticola comb. nov. and Falsiroseomonas oleicola comb. nov

A Gram-stain-negative, short rod-shaped strain, MDT2-1-1T, was isolated from cryoconite samples collected from the Midui glacier in Tibet, China. It grew aerobically from 7 to 40 °C, within a pH range of 6.0-10.0, and in NaCl concentration of 0 to 1.0% (w/v). The pairwise 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization values between strains MDT2-1-1T and Sabulicella rubraurantiaca SYSU D01096T were 99.4%, 89.7% and 38.9%, respectively. Considering the results from phylogeny, phenotypic and genotypic data, strain MDT2-1-1T (=CGMCC 1.11170T = NBRC 110485T) was suggested to represent a novel species of the genus Sabulicella, for which the name Sabulicella glaciei sp. nov. is proposed. Furthermore, based on the phylogenomic analysis, it is recommended that Roseomonas rubea, Roseomonas ponticola and Roseomonas oleicola be reclassified as Neoroseomonas rubea comb. nov., Falsiroseomonas ponticola comb. nov. and Falsiroseomonas oleicola comb. nov., respectively. Considering the illegitimate status of the genera names Pararoseomonas and Pseudoroseomonas, the species within the genera Pararoseomonas and Pseudoroseomonas should be transferred to Muricoccus and Teichococcus, respectively. Therefore, we proposed the following new combinations: Muricoccus aeriglobus comb. nov., Muricoccus aerilatus comb. nov., Muricoccus harenae comb. nov., Muricoccus nepalensis comb. nov., Muricoccus pecuniae comb. nov., Muricoccus radiodurans comb. nov., Muricoccus vinaceus comb. nov., Teichococcus aerofrigidensis comb. nov., Teichococcus aerophilus comb. nov., Teichococcus aestuarii comb. nov., Teichococcus cervicalis comb. nov., Teichococcus coralli comb. nov., Teichococcus deserti comb. nov., Teichococcus globiformis comb. nov., Teichococcus hibiscisoli comb. nov., Teichococcus musae comb. nov., Teichococcus oryzae comb. nov., Teichococcus rhizosphaerae comb. nov., Teichococcus ruber comb. nov., Teichococcus suffuscus comb. nov., Teichococcus vastitatis comb. nov., and Teichococcus wenyumeiae comb. nov.

Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide

The MHYT domain, identified over two decades ago for its potential to detect diatomic gases like CO, O2 or NO, has awaited experimental validation as a protein sensory domain. Here, we characterize the MHYT domain-containing transcriptional regulator CoxC, which governs the expression of the cox genes responsible for aerobic CO oxidation in the carboxidotrophic bacterium Afipia carboxidovorans OM5. The C-terminal LytTR-type DNA-binding domain of CoxC binds to an operator region consisting of three direct repeats sequences overlapping the -35 box at the target PcoxB promoter, which is consistent with the role of CoxC as a specific transcriptional repressor of the cox genes. Notably, the N-terminal transmembrane MHYT domain endows CoxC with the ability to sense CO as an effector molecule, as demonstrated by the relief of CoxC-mediated repression and binding to the PcoxB promoter upon CO exposure. Furthermore, copper serves as the essential divalent cation for the interaction of CO with CoxC, thereby confirming previous hypothesis regarding the role of copper in the gas-sensing mechanism of MHYT domains. CoxC represents the prototype of a novel subfamily of single-component LytTR transcriptional regulators, characterized by the fusion of a DNA-binding domain with a membrane-bound MHYT sensor domain.

The Impact of the Major Endoribonucleases RNase E and RNase III and of the sRNA StsR on Photosynthesis Gene Expression in Rhodobacter sphaeroides Is Growth-Phase-Dependent

Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment-protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen and light has been investigated for decades, with a focus on the regulation of transcription. However, many studies have also revealed the importance of regulated mRNA processing. This study analyzes the phenotypes of wild type and mutant strains and compares global RNA-seq datasets to elucidate the impact of ribonucleases and the small non-coding RNA StsR on photosynthesis gene expression in Rhodobacter. Most importantly, the results demonstrate that, in particular, the role of ribonuclease E in photosynthesis gene expression is strongly dependent on growth phase.

A systematic review and meta-analysis of comparative clinical studies on antibiotic treatment of brucellosis

Brucellosis is a difficult to treat infection that requires antibiotic combinations administered over several weeks for clearance of infection and relapse prevention. This systematic review summarizes current evidence for antibiotic treatment of human brucellosis. PubMed, EMBASE, Scopus, CINAHL, Web of Science, and China Academic Journal databases were searched for prospective studies that had compared different antibiotic regimens for treating human brucellosis in the last 25 years. Thirty-four studies recruiting 4182 participants were eligible. Standard dual therapy with doxycycline + rifampicin had a higher risk of treatment failure compared to triple therapy which added streptomycin (RR: 1.98, 95% CI 1.17-3.35, p = 0.01) or levofloxacin (RR: 2.98, 95% CI 1.67-5.32, p = 0.0002), but a similar or lower risk compared to alternative dual antibiotic combinations (p > 0.05). The same combination had a higher risk of relapses compared to triple therapy which added streptomycin (RR: 22.12, 95% CI 3.48-140.52, p = 0.001), or levofloxacin (RR: 4.61, 95% CI 2.20-9.66, p < 0.0001), but a similar or lower risk compared to other dual antibiotic combinations (p > 0.05). Triple antibiotic therapy is more effective than standard dual therapy with rifampicin and doxycycline. However, the latter is also efficacious and suitable for uncomplicated disease.

OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

Mannitol as a Growth Substrate for Facultative Methylotroph Methylobrevis pamukkalensis PK2

Biochemistry of carbon assimilation in aerobic methylotrophs growing on reduced C1 compounds has been intensively studied due to the vital role of these microorganisms in nature. The biochemical pathways of carbon assimilation in methylotrophs growing on multi-carbon substrates are insufficiently explored. Here we elucidated the metabolic route of mannitol assimilation in the alphaproteobacterial facultative methylotroph Methylobrevis pamukkalensis PK2. Two key enzymes of mannitol metabolism, mannitol-2-dehydrogenase (MTD) and fructokinase (FruK), were obtained as His-tagged proteins by cloning and expression of mtd and fruK genes in Escherichia coli and characterized. Genomic analysis revealed that further transformation of fructose-6-phosphate proceeds via the Entner-Doudoroff pathway. During growth on mannitol + methanol mixture, the strain PK2 consumed both substrates simultaneously demonstrating independence of C1 and C6 metabolic pathways. Genome screening showed that genes for mannitol utilization enzymes are present in other alphaproteobacterial methylotrophs predominantly capable of living in association with plants. The capability to utilize a variety of carbohydrates (sorbitol, glucose, fructose, arabinose and xylose) suggests a broad adaptability of the strain PK2 to live in environments where availability of carbon substrate dynamically changes.

The microbiome compositional and functional differences between rectal mucosa and feces

In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population.

IMPORTANCE

This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.

Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L

Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and the influence of nickel ions on this process were studied. On the basis of whole-genome and polyphasic taxonomy, the bacterium Rsf11 represent a novel species of the genus Neorhizobium, so the name Neorhizobium phenanthreniclasticum sp. nov. was proposed. Analysis of phenanthrene degradation by the Rsf1 strain revealed 1-hydroxy-2-naphthoic acid as the key intermediate and the activity of two enzymes apparently involved in PAH degradation. It was also shown that the nickel resistance of Rsf11 was connected with the extracellular adsorption of metal by EPS. The joint presence of phenanthrene and nickel in the medium reduced the degradation of PAH by the microorganism, apparently due to the inhibition of microbial growth but not due to the inhibition of the activity of the PAH degradation enzymes. Genes potentially involved in PAH catabolism and nickel resistance were discovered in the microorganism studied. N. phenanthreniclasticum strain Rsf11 can be considered as a promising candidate for use in the bioremediation of mixed PAH-heavy-metal contamination.

Molecular typing methods to characterize Brucella spp. from animals: A review

Brucellosis is an infectious disease of animals that can infect humans. The disease causes significant economic losses and threatens human health. A timely and accurate disease diagnosis plays a vital role in the identification of brucellosis. In addition to traditional diagnostic methods, molecular methods allow diagnosis and typing of the causative agent of brucellosis. This review will discuss various methods, such as Bruce-ladder, Suiladder, high-resolution melt analysis, restriction fragment length polymorphism, multilocus sequence typing, multilocus variable-number tandem repeat analysis, and whole-genome sequencing single-nucleotide polymorphism, for the molecular typing of Brucella and discuss their advantages and disadvantages.

Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.

Microbial influence on the larval survival of Japanese eel Anguilla japonica: Antibiotic-mediated alterations and biomarker isolation

In rearing systems for the Japanese eel Anguilla japonica, although it is assumed that microorganisms influence larval survival and mortality, particularly during the early stages of growth, the effects of bacterial communities on larval survival have yet to be sufficiently determined. In this study, we compared the bacterial communities associated with larval survival at three stages of eel growth. To artificially alter bacterial communities and assess larval survival, eel larvae were treated with 11 types of antibiotic, and larval survival and bacterial characteristics were compared between the antibiotic-treated and antibiotic-free control groups. Throughout the three growth stages, eels treated with four antibiotics (polymyxin B, tetracycline, novobiocin, and erythromycin) had survival rates higher than those in the control groups. The bacterial communities of surviving larvae in the control and antibiotic groups and dead larvae in the control groups were subsequently analyzed using 16S rRNA gene amplicon sequencing. PERMANOVA analysis indicated that these three larval groups were characterized by significantly different bacterial communities. We identified 14 biomarker amplicon sequence variants (ASVs) of bacterial genera such as Oceanobacter, Alcanivorax, Marinobacter, Roseibium, and Sneathiella that were enriched in surviving larvae in the antibiotic treatment groups. In contrast, all four biomarker ASVs enriched in dead larvae of the control groups were from bacteria in the genus Vibrio. Moreover, 52 bacterial strains corresponding to nine biomarkers were isolated using a culture method. To the best of our knowledge, this is the first study to evaluate the bacterial communities associated with the survival and mortality of larvae in during the early stages of Japanese eel growth and to isolate biomarker bacterial strains. These findings will provide valuable insights for enhancing larval survival in the eel larval rearing systems from a microbiological perspective.

Sulfoquinovosyl diacylglycerol is required for dimerisation of the Rhodobacter sphaeroides reaction centre-light harvesting 1 core complex

The reaction centre-light harvesting 1 (RC-LH1) core complex is indispensable for anoxygenic photosynthesis. In the purple bacterium Rhodobacter (Rba.) sphaeroides RC-LH1 is produced both as a monomer, in which 14 LH1 subunits form a C-shaped antenna around 1 RC, and as a dimer, where 28 LH1 subunits form an S-shaped antenna surrounding 2 RCs. Alongside the five RC and LH1 subunits, an additional polypeptide known as PufX provides an interface for dimerisation and also prevents LH1 ring closure, introducing a channel for quinone exchange that is essential for photoheterotrophic growth. Structures of Rba. sphaeroides RC-LH1 complexes revealed several new components; protein-Y, which helps to form the quinone channel; protein-Z, of unknown function and seemingly unique to dimers; and a tightly bound sulfoquinovosyl diacylglycerol (SQDG) lipid that interacts with two PufX arginine residues. This lipid lies at the dimer interface alongside weak density for a second molecule, previously proposed to be an ornithine lipid. In this work we have generated strains of Rba. sphaeroides lacking protein-Y, protein-Z, SQDG or ornithine lipids to assess the roles of these previously unknown components in the assembly and activity of RC-LH1. We show that whilst the removal of either protein-Y, protein-Z or ornithine lipids has only subtle effects, SQDG is essential for the formation of RC-LH1 dimers but its absence has no functional effect on the monomeric complex.

Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand

A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).

Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov., two novel Erythrobacteraceae species isolated from tidal flat sediments

Two Gram-stain-negative, rod-shaped, non-motile, aerobic and carotenoid-producing strains, belonging to the family Erythrobacteraceae, designated as H149T and Z2T, were isolated from tidal flat sediment samples collected in Hainan and Zhejiang, PR China, respectively. Growth of strain H149T occurred at 15-42 °C, 0-10.0 % (w/v) NaCl, and pH 6.0-8.5, with the optima at 35-37 °C, 3.0-3.5 % (w/v) NaCl and pH 7.0. Strain Z2T grew at 15-37 °C, 0-6.0 % (w/v) NaCl, and pH 6.0-9.5, with the optima at 25-30 °C, 0.5-1.0 % (w/v) NaCl and pH 6.0-6.5. Ubiquinone-10 was the sole ubiquinone in two strains. The predominant cellular fatty acids of strain H149T were C16 : 0, summed feature 3 and summed feature 8, while those of strain Z2T were C17 : 1  ω6c, summed feature 3 and summed feature 8. Strains H149T and Z2T shared diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid as major polar lipids. The 16S rRNA gene sequence identity analysis indicated that strain H149T had the highest sequence identity of 98.4 % with Aurantiacibacter odishensis KCTC 23981T, and strain Z2T had that of 98.2 % with Qipengyuania pacifica NZ-96T. Phylogenetic trees based on 16S rRNA gene and core-genome sequences revealed that strains H149T and Z2T formed two independent clades in the genera Aurantiacibacter and Qipengyuania, respectively. Strain H149T had average nucleotide identity values of 74.0-81.3 % and in silico DNA-DNA hybridization values of 18.5-23.1 % with Aurantiacibacter type strains, while strain Z2T had values of 73.3-78.7 % and 14.5-33.3 % with Qipengyuania type strains. The genomic DNA G+C contents of strains H149T and Z2T were 64.3 and 61.8 %, respectively. Based on the genetic, genomic, phylogenetic, physiological and chemotaxonomic results, strains H149T (=KCTC 8397T=MCCC 1K08920T) and Z2T (=KCTC 8396T=MCCC 1K08946T) are concluded to represent two novel Erythrobacteraceae species for which the names Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov. are proposed, respectively.

Roseibium algae sp. nov., isolated from a marine alga (Grateloupia sp.)

A novel Gram-stain-negative, rod-shaped, non-spore-forming, aerobic, motile bacterium with a single polar or subpolar flagellum, designated strain H3510T, was isolated from marine alga collected on sea shore of Yantai, PR China. The organism grew optimally at 28 °C and pH 7.0 and in presence of 3.0 % (w/v) NaCl. The strain exhibited positive catalase activity but negative oxidase and nitrate reduction activities. The predominant cellular fatty acids were C18 : 1  ω7c and/or C18 : 1  ω6c, 11-methyl C18 : 1  ω7c, and C16 : 0. Additionally, the major polar lipids were phosphatidylglycerol, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, and phosphatidylethanolamine; the respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content of strain H3510T was 54.2%. The novel strain showed the closest relationship with Roseibium polysiphoniae KMM 9699T with 98.2 % 16S rRNA gene sequence similarity. The calculated values for average nucleotide identity and DNA-DNA hybridization between strain H3510T and the phylogenetically related Roseibium species were in the range of 71.3-74.9 % and 13.7-19.9 %, respectively. Based on polyphasic analyses, strain H3510T was identified as representing a novel species of the genus Roseibium, for which the name Roseibium algae sp. nov. is proposed. The type strain is H3510T (=KCTC 8206T=MCCC 1K04325T). The heterologously expressed inositol 2-dehydrogenase gene from strain H3510T displayed high oxidation activity on myo-inositol and showed potential in the production of rare stereoisomers of inositol, such as scyllo-inositol.

Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality

Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.

Discovery of novel treponemes associated with pododermatitis in elk (Cervus canadensis)

Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk (Cervus canadensis) populations in the northwestern USA, with Treponema spp. consistently implicated in the lesion development. However, identifying species-specific Treponema strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, in silico genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled Treponema genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species-Treponema pedis and Treponema phagedenis. Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other Treponema genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel Treponema genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCETreponema spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of Treponema from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and in silico genome reconstruction to identify novel Treponema genomospecies from elk with pododermatitis. The discovery of the novel Treponema species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the Treponemataceae consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.

Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production

Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm-1 generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.

Roseiterribacter gracilis gen. nov., sp. nov., a novel filterable alphaproteobacterium isolated from soil using a gel-filled microwell array device

Our previous studies indicate the abundant and diverse presence of yet-to-be-cultured microorganisms in the micropore-filtered fractions of various environmental samples. Here, we isolated a novel bacterium (designated as strain TMPK1T) from a 0.45-μm-filtered soil suspension by using a gel-filled microwell array device comprising 900 microwells and characterized its phylogenetic and physiological features. This strain showed low 16S rRNA gene sequence identities (<91%) and low average nucleotide identity values (<70%) to the closest validly described species, and belonged to a novel-family-level lineage within the order Rhodospirillales of Alphaproteobacteria. Strain TMPK1T exhibited small cell sizes (0.08-0.23 μm3) and had a high cyclopropane fatty acid content (>13%), and these characteristics were differentiated from other Rhodospirillales bacteria. A comprehensive habitability search using amplicon datasets suggested that TMPK1T and its close relatives are mainly distributed in soil and plant-associated environments. Based on these results, we propose that strain TMPK1T represents a novel genus and species named Roseiterribacter gracilis gen. nov., sp. nov. (JCM 34627T = KCTC 82790T). We also propose Roseiterribacteraceae fam. nov. to accommodate the genus Roseiterribacter.

Bosea rubneri sp. nov. Isolated from Organically Grown Allium cepa

Strain ZW T0_25T was isolated from an onion sample (Allium cepa var. Hytech F1) within a storage trial and proofed to be a novel, aerobic, Gram-stain negative, rod-shaped bacterial strain. Analyses of the 16S rRNA gene sequence and of the whole draft genome sequences, i.e., digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) showed that this strain represents a new species of the genus Bosea. The genome size of strain ZW T0_25T is 6.19 Mbp, and the GC content is 66.9%. As whole cell sugars, rhamnose, ribose and glucose were identified. Ubiquinone Q-10 is the major respiratory quinone with 97.8%. Polar lipids in strain ZW T0_25T are composed of one phosphatidylethanolamine, one phosphatidylglycerol, one aminophospholipid, two aminolipids, one glycolipid and two phospholipids whereas the fatty acid profile predominantly consists of C18:1 w7c (63.3%), C16:1 w7c (19.5%) and C16:0 (7.1%). Phenotypic traits were tested in the wet lab as well as predicted in silico from genome data. Therefore, according to this polyphasic approach, the new name Bosea rubneri sp. nov. with the type strain ZW T0_25T (= DSM 116094 T = LMG 33093 T) is proposed.

Anaerobic co-metabolic biodegradation of pharmaceuticals and personal care products driven by glycerol fermentation

Anaerobic digestion in two sequential phases, acidogenesis and methanogenesis, has been shown to be beneficial for enhancing the biomethane generation from wastewater. In this work, the application of glycerol (GOH) as a fermentation co-substrate during the wastewater treatment was evaluated on the biodegradation of different pharmaceuticals and personal care products (PPCPs). GOH co-digestion during acidogenesis led to a significant increase in the biodegradation of acetaminophen (from 78 to 89%), ciprofloxacin (from 25 to 46%), naproxen (from 73 to 86%), diclofenac (from 36 to 48%), ibuprofen (from 65 to 88%), metoprolol (from 45 to 59%), methylparaben (from 64 to 78%) and propylparaben (from 68 to 74%). The heterotrophic co-metabolism of PPCPs driven by glycerol was confirmed by the biodegradation kinetics, in which kbio (biodegradation kinetics constant) values increased from 0.18 to 2.11 to 0.27-3.60 L g-1-VSS d-1, for the operational phases without and with GOH, respectively. The assessment of metabolic pathways in each phase revealed that the prevalence of aromatic compounds degradation, metabolism of xenobiotics by cytochrome P450, and benzoate degradation routes during acidogenesis are key factors for the enzymatic mechanisms linked to the PPCPs co-metabolism. The phase separation of anaerobic digestion was effective in the PPCPs biodegradation, and the co-fermentation of glycerol provided an increase in the generation potential of biomethane in the system (energetic potential of 5.0 and 6.3 kJ g-1-CODremoved, without and with GOH, respectively). This study showed evidence that glycerol co-fermentation can exert a synergistic effect on the PPCPs removal during anaerobic digestion mediated by heterotrophic co-metabolism.

Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. isolated from coral tissue: proposal of two new families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov

A genome-based polyphasic approach was used to determine the taxonomic status of two novel bacterial strains, SCSIO 12594T and SCSIO 12813T, isolated from tissues of a coral. Both strains were Gram-stain-negative and facultatively anaerobic. The genome sizes of strains SCSIO 12594T and SCSIO 12813T were 3.9 Mb and 4.1 Mb, respectively, and they possessed DNA G+C contents of 55.1 and 46.2 mol%, respectively . Both strains were found to be catalase- and oxidase-positive, while SCSIO 12594T also could hydrolyse starch. SCSIO 12594T was observed to grow at between 20 and 37 °C (optimally at 25 °C) and at a pH range from 6 to 7 and in the presence of 3-7 % (w/v) NaCl. The growth of SCSIO 12813T required seawater and occurred at 20-30 °C (optimum, 25 °C), pH 5-8 (optimum, pH 6-7) and in the presence of 3-3.7 % (w/v) NaCl. The results of 16S rRNA gene-based phylogenetic analysis indicated that SCSIO 12594T shared 92.97 % or less sequence similarity with its closest relatives Rhodobium gokarnense JA173T and other members of the order Hyphomicrobiales. The results of 16S rRNA sequences-based phylogenetic analysis of SCSIO 12813T indicated that Croceimicrobium hydrocarbonivorans A20-9T (89.34 %) was the most closely related species. SCSIO 12594T and SCSIO 12813T can be readily separated from their closest relatives, as indicated by the results of phylogenomic analysis, low average nucleotide indexes, average amino acid identity, digital DNA-DNA hybridisation (dDDH) similarities and associated phenotypic and chemical data. Consequently, the two coral isolates are considered to represent two novel genera and species for which the names Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. are proposed, the type strains are SCSIO 12594T (= JCM 35320T = GDMCC 1.3060T) and SCSIO 12813T (= JCM 35373T = GDMCC 1.3063T), respectively. In addition, two novel families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov are proposed to accommodate Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov., respectively.

Getting to the point: unipolar growth of Hyphomicrobiales

The governing principles and suites of genes for lateral elongation or incorporation of new cell wall material along the length of a rod-shaped cell are well described. In contrast, relatively little is known about unipolar elongation or incorporation of peptidoglycan at one end of the rod. Recent work in three related model systems of unipolar growth (Agrobacterium tumefaciens, Brucella abortus, and Sinorhizobium meliloti) has clearly established that unipolar growth in the Hyphomicrobiales order relies on a set of genes distinct from the canonical elongasome. Polar incorporation of envelope components relies on homologous proteins shared by the Hyphomicrobiales, reviewed here. Ongoing and future work will reveal how unipolar growth is integrated into the alphaproteobacterial cell cycle and coordinated with other processes such as chromosome segregation and cell division.

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.

Rhizosphere competent inoculants modulate the apple root-associated microbiome and plant phytoalexins

Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD. KEY POINTS: • Rhizosphere competent inoculants modulated the microbiome (mainly fungi) • Inoculants reduced relative abundance of Enterobacteriaceae in the ARD rhizoplane • Inoculants increased phytoalexin content in roots, stronger in grass than ARD soil.

Rapid Identification of Brucella Genus and Species In Silico and On-Site Using Novel Probes with CRISPR/Cas12a

Human brucellosis caused by Brucella is a widespread zoonosis that is prevalent in many countries globally. The high homology between members of the Brucella genus and Ochrobactrum spp. often complicates the determination of disease etiology in patients. The efficient and reliable identification and distinction of Brucella are of primary interest for both medical surveillance and outbreak purposes. A large amount of genomic data for the Brucella genus was analyzed to uncover novel probes containing single-nucleotide polymorphisms (SNPs). GAMOSCE v1.0 software was developed based on the above novel eProbes. In conjunction with clinical requirements, an RPA-Cas12a detection method was developed for the on-site determination of B. abortus and B. melitensis by fluorescence and lateral flow dipsticks (LFDs). We demonstrated the potential of these probes for rapid and accurate detection of the Brucella genus and five significant Brucella species in silico using GAMOSCE. GAMOSCE was validated on different Brucella datasets and correctly identified all Brucella strains, demonstrating a strong discrimination ability. The RPA-Cas12a detection method showed good performance in detection in clinical blood samples and veterinary isolates. We provide both in silico and on-site methods that are convenient and reliable for use in local hospitals and public health programs for the detection of brucellosis.

Abundance, Characterization and Diversity of Culturable Anoxygenic Phototrophic Bacteria in Manitoban Marshlands

Marshes are an important ecosystem, acting as a biodiversity hotspot, a carbon sink and a bioremediation site, breaking down anthropogenic waste such as antibiotics, metals and fertilizers. Due to their participation in these metabolic activities and their capability to contribute to primary productivity, the microorganisms in such habitats have become of interest to investigate. Since Proteobacteria were previously found to be abundant and the waters are well aerated and organic-rich, this study on the presence of anoxygenic phototrophic bacteria, purple non-sulfur bacteria and aerobic anoxygenic phototrophs in marshes was initiated. One sample was collected at each of the seven Manitoban sites, and anoxygenic phototrophs were cultivated and enumerated. A group of 14 strains, which represented the phylogenetic diversity of the isolates, was physiologically investigated further. Aerobic anoxygenic phototrophs and purple non-sulfur bacteria were present at each location, and they belonged to the α- and β-Proteobacteria subphyla. Some were closely related to known heavy metal reducers (Brevundimonas) and xenobiotic decomposers (Novosphingobium and Sphingomonas). All were able to synthesize the photosynthetic complexes aerobically. This research highlights the diversity of and the potential contributions that anoxygenic phototrophs make to the essential functions taking place in wetlands.

Delay in the diagnosis of Brucella abortus bacteremia in a nonendemic country: a case report

BACKGROUND

It is challenging to diagnose brucellosis in nonendemic regions because it is a nonspecific febrile disease. The accurate identification of Brucella spp. in clinical microbiology laboratories (CMLs) continues to pose difficulties. Most reports of misidentification are for B. melitensis, and we report a rare case of misidentified B. abortus.

CASE PRESENTATION

A 67-year-old man visited an outpatient clinic complaining of fatigue, fever, and weight loss. The patient had a history of slaughtering cows with brucellosis one year prior, and his Brucella antibody tests were negative twice. After blood culture, the administration of doxycycline and rifampin was initiated. The patient was hospitalized due to a positive blood culture. Gram-negative coccobacilli were detected in aerobic blood culture bottles, but the CML's lack of experience with Brucella prevented appropriate further testing. Inaccurate identification results were obtained for a GN ID card of VITEK 2 (bioMérieux, USA) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using a MALDI Biotyper (Bruker, Germany). The strain showed 100.0% identity with Brucella spp. according to 16S rRNA sequencing. MALDI-TOF MS peaks were reanalyzed using the CDC MicrobeNet database to determine Brucella spp. (score value: 2.023). The patient was discharged after nine days of hospitalization and improved after maintaining only doxycycline for six weeks. The isolate was also identified as Brucella abortus by genomic evidence.

CONCLUSION

Automated identification instruments and MALDI-TOF MS are widely used to identify bacteria in CMLs, but there are limitations in accurately identifying Brucella spp. It is important for CMLs to be aware of the possibility of brucellosis through communication with clinicians. Performing an analysis with an additional well-curated MALDI-TOF MS database such as Bruker security-relevant (SR) database or CDC MicrobeNet database is helpful for quickly identifying the genus Brucella.

SeqCode facilitates naming of South African rhizobia left in limbo

South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.

Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species

BACKGROUD

The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated.

RESULTS

The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus.

CONCLUSION

The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus

Bacteria use CRISPR Cas systems to defend against invading foreign nucleic acids, e.g., phage genomes, plasmids or mobile genetic elements. Some CRISPR Cas systems were reported to have physiological importance under a variety of abiotic stress conditions. We used physiological tests under different stress conditions and RNA-seq analyses to address the possible function of the RNA-targeting class 2 type VI CRISPR Cas system of the facultative phototrophic α-proteobacterium Rhodobacter capsulatus. Expression of the system was low under exponential non-stress conditions and high during oxidative stress, membrane stress and in stationary phase. Induction of the CRISPR Cas system in presence of a target protospacer RNA resulted in a growth arrest of R. capsulatus. RNA-seq revealed a strong alteration of the R. capsulatus transcriptome when cas13a was induced in presence of a target protospacer. RNA 5' end mapping indicated that the CRISPR Cas-dependent transcriptome remodeling is accompanied by fragmentation of cellular RNAs, e.g., for mRNAs originating from a genomic locus which encodes multiple ribosomal proteins and the RNA polymerase subunits RpoA, RpoB and RpoC. The data suggest a function of this CRISPR Cas system in regulated growth arrest, which may prevent the spread of phages within the population.

Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation

BACKGROUND

The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation.

RESULTS

This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy.

CONCLUSIONS

Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.

Terrirubrum flagellatum gen. nov., sp. nov. of Terrirubraceae fam. nov. and Lichenibacterium dinghuense sp. nov. from forest soil and proposal of Rhodoblastaceae fam. nov

Two Gram-negative, aerobic, rod-shaped bacterial strains, 7MK25T and 6Y81T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain 7MK25T showed the highest similarity (93.6 %) to Methyloferula stellata AR4T, followed by Bosea thiooxidans DSM 9653T (93.3 %). Strain 6Y81T had the highest similarity of 97.9 % to Lichenibacterium minor RmlP026T, followed by Lichenibacterium ramalinae RmlP001T (97.2 %). Phylogenomic analysis using the UBCG and PhyloPhlAn methods consistently showed that strain 7MK25T formed a sister clade to Boseaceae, while strain 6Y81T formed an independent clade within the genus Lichenibacterium, both in the order Hyphomicrobiales. The digital DNA-DNA hybridization and average nucleotide identity values between strains 7MK25T, 6Y81T and their close relatives were in the ranges of 19.1-29.9 % and 72.5-85.5 %, respectively. The major fatty acids of 7MK25T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C19 : 0 cyclo ω8c, C16 : 0 and C17 : 0 cyclo, while those of 6Y81T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0 and C16 : 0 3-OH. Strains 7MK25T and 6Y81T took diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as their dominant polar lipids, and Q-10 as their major respiratory quinone. On the basis of phenotypic and phylogenetic data, strain 7MK25T is proposed to represent a novel species of a novel genus with name Terrirubrum flagellatum gen. nov., sp. nov., within a novel family Terrirubraceae fam. nov., with 7MK25T (=KCTC 62738T=GDMCC 1.1452T) as its type strain. Strain 6Y81T represents a novel species in the genus Lichenibacterium, for which the name Lichenibacterium dinghuense sp. nov. (type strain 6Y81T=KACC 21 727T=GDMCC 1.2176T) is proposed. Rhodoblastaceae fam. nov. with Rhodoblastus as the type genus is also proposed to solve the non-monophylectic problem of the family Roseiarcaceae.

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

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

Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1

Aminophosphonates, like glyphosate (GS) or metal chelators such as ethylenediaminetetra(methylenephosphonic acid) (EDTMP), are released on a large scale worldwide. Here, we have characterized a bacterial strain capable of degrading synthetic aminophosphonates. The strain was isolated from LC/MS standard solution. Genome sequencing indicated that the strain belongs to the genus Ochrobactrum. Whole-genome classification using pyANI software to compute a pairwise ANI and other metrics between Brucella assemblies and Ochrobactrum contigs revealed that the bacterial strain is designated as Ochrobactrum sp. BTU1. Degradation batch tests with Ochrobactrum sp. BTU1 and the selected aminophosphonates GS, EDTMP, aminomethylphosphonic acid (AMPA), iminodi(methylene-phosphonic) (IDMP) and ethylaminobis(methylenephosphonic) acid (EABMP) showed that the strain can use all phosphonates as sole phosphorus source during phosphorus starvation. The highest growth rate was achieved with AMPA, while EDTMP and GS were least supportive for growth. Proteome analysis revealed that GS degradation is promoted by C-P lyase via the sarcosine pathway, i.e., initial cleavage at the C-P bond. We also identified C-P lyase to be responsible for degradation of EDTMP, EABMP, IDMP and AMPA. However, the identification of the metabolite ethylenediaminetri(methylenephosphonic acid) via LC/MS analysis in the test medium during EDTMP degradation indicates a different initial cleavage step as compared to GS. For EDTMP, it is evident that the initial cleavage occurs at the C-N bond. The detection of different key enzymes at regulated levels, form the bacterial proteoms during EDTMP exposure, further supports this finding. This study illustrates that widely used and structurally more complex aminophosphonates can be degraded by Ochrobactrum sp. BTU1 via the well-known degradation pathways but with different initial cleavage strategy compared to GS.

Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding of microbial diversity and evolution. The introduction of molecular techniques, particularly DNA sequencing and genomics, has transformed our perception of prokaryotic diversity. In the past two decades, advancements in genome sequencing have transitioned from traditional methods to a genome-based taxonomic framework, not only to define species, but also higher taxonomic ranks. As technology and databases rapidly expand, maintaining updated standards is crucial. This work seeks to revise the 2018 guidelines for applying genome sequencing data in microbial taxonomy, adapting minimal standards and recommendations to reflect technological progress during this period.

Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov

A microaerophilic, Gram-negative, motile, and spiral-shaped bacterium, designated Y-M2T, was isolated from oil sludge of Shengli oil field. The optimal growth condition of strain Y-M2T was at 25 °C, pH 7.0, and in the absence of NaCl. The major polar lipid was phosphatidylethanolamine. The main cellular fatty acid was iso-C17  :  0 3-OH. It contained Q-9 and Q-10 as the predominant quinones. The DNA G+C content was 68.1 mol%. Strain Y-M2T showed the highest 16S rRNA gene sequence similarity to Telmatospirillum siberiense 26-4bT (91.1 %). Phylogenetic analyses based on 16S rRNA gene and genomes showed that strain Y-M2T formed a distinct cluster in the order Rhodospirillales. Genomic analysis showed that Y-M2T possesses a complete nitrogen-fixation cluster which is phylogenetically close to that of methanogene. The nif cluster, encompassing the nitrogenase genes, was found in every N2-fixing strain within the order Rhodospirillales. Phylogeny, phenotype, chemotaxonomy, and genomic results demonstrated that strain Y-M2T represents a novel species of a novel genus in a novel family Oleispirillaceae fam. nov. in the order Rhodospirillales, for which the name Oleispirillum naphthae gen. nov., sp. nov. was proposed. The type strain is Y-M2T (=CCAM 827T=JCM 34765T).

Structure, Physicochemical Properties and Biological Activity of Lipopolysaccharide from the Rhizospheric Bacterium Ochrobactrum quorumnocens T1Kr02, Containing d-Fucose Residues

Lipopolysaccharides (LPSs) are major components of the outer membranes of Gram-negative bacteria. In this work, the structure of the O-polysaccharide of Ochrobactrum quorumnocens T1Kr02 was identified by nuclear magnetic resonance (NMR), and the physical-chemical properties and biological activity of LPS were also investigated. The NMR analysis showed that the O-polysaccharide has the following structure: →2)-β-d-Fucf-(1→3)-β-d-Fucp-(1→. The structure of the periplasmic glucan coextracted with LPS was established by NMR spectroscopy and chemical methods: →2)-β-d-Glcp-(1→. Non-stoichiometric modifications were identified in both polysaccharides: 50% of d-fucofuranose residues at position 3 were O-acetylated, and 15% of d-Glcp residues at position 6 were linked with succinate. This is the first report of a polysaccharide containing both d-fucopyranose and d-fucofuranose residues. The fatty acid analysis of the LPS showed the prevalence of 3-hydroxytetradecanoic, hexadecenoic, octadecenoic, lactobacillic, and 27-hydroxyoctacosanoic acids. The dynamic light scattering demonstrated that LPS (in an aqueous solution) formed supramolecular particles with a size of 72.2 nm and a zeta-potential of -21.5 mV. The LPS solution (10 mkg/mL) promoted the growth of potato microplants under in vitro conditions. Thus, LPS of O. quorumnocens T1Kr02 can be recommended as a promoter for plants and as a source of biotechnological production of d-fucose.