Microbiology Resource Announcements

Here we report the complete organellar genome sequences of Medakamo hakoo, a green alga identified in freshwater in Japan. It has 90.8-kb plastid and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein coding genes, respectively, representing the smallest organellar genome among currently known core Trebouxiophyceae.

The draft genome sequence of the soil bacterium Pedococcus sp. 5OH_020, isolated on a natural vitamin B12 analog, contains 4.4 Mbp with 4,108 protein-coding genes. Its genome encodes B12-dependent enzymes including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests it is a novel species within the genus Pedococcus.

A hybrid sequencing approach, using short and long reads sequencing, was employed for characterizing the genomes of the free-living amoeba host Vermamoeba vermiformis, along with its Dependentiae endosymbiont Vermiphilus pyriformis. The amoeba host reconstructed nuclear genome is 39.5 Mb, and its full mitochondrial genome is 61.7 kb. The closed, circular genome of the Dependentiae endosymbiont Vermiphilus pyriformis, naturally infecting V. vermiformis is 1.1 Mb.

Here we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 media.

We present the complete genome sequences of two strains of Teredinibacter turnerae, SR01903 and SR02026, shipworm endosymbionts isolated from the gills of Lyrodus pedicellatus and Teredo bartschi, respectively, and derived from Oxford Nanopore sequencing. These sequences will aid in the comparative genomics of shipworm endosymbionts and understanding of host-symbiont selection.

The genus Sinorhizobium comprises rhizobia that fix nitrogen in symbiosis with legumes. To support taxonomic studies of this genus and of rhizobia more broadly, we report complete genome sequences and annotations for the species type strains Sinorhizobium garamanticum LMG 24692T and Sinorhizobium numidicum LMG 27395T and CIP 109850T. Average nucleotide identity and core-genome phylogenetic analyses confirm that S. garamanticum and S. numidicum represent distinct species.

We report the complete genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database (GTDB) indicates that Fusobacterium watanabei genomes are part of the "Fusobacterium nucleatum_J" group, which also encompasses the previously published FNU strain and Fna C1 isolates.

We report the draft genomes of four Kluyveromyces marxianus isolates obtained from the elaboration process of henequen (Agave fourcroydes) mezcal, a Mexican alcoholic beverage. The average nucleotide identity (ANI) analysis revealed that isolates derived from agave plants are distinct from those from other environments, including agave fermentations.

Janthinobacterium is a genus of Gram-negative environmental bacteria that survive extreme conditions by forming biofilms and producing pigments. Janthinobacterium sp. LS2A, an extremophile isolated from soil in the Chilean Patagonia, contains seven known biosynthetic gene clusters, including the purple pigment violacein, which may aid in its survival in harsh environments.

We report the genome sequence of Bacillus paranthracis SCM10-01, isolated from a wild neotropical bird (Synallaxis cabanisi) collected in Peru. The assembly yielded one chromosome, three plasmids, and Bacillus phage SCM10. Genomic screening identified complete hemolysin BL, nonhemolytic enterotoxin operons, and cytotoxin K2, but no anthrax-associated toxin or capsule genes.

We report the complete CDS of five viruses: an iflavirus, a protoambidensovirus and three microviruses),which were detected by viromics surveillance of mosquitoes (Aedes albopictus and Culex quinquefasciatus) from the Reunion Island. We detected the protoambidensovirus, which belongs to aclade previously reported only in C. pipiens, in A. albopictus.

We isolated a gammaproteobacterial methanotrophic strain FWC3, from canal sediment from Western India. The strain oxidizes methane and can also grow on methanol. The draft genome of the same was sequenced which showed a size of [~]3.4 Mbp and 63% GC content. FWC3 is a coccoid, pale pink pigmented methanotroph and is seen in the form of diplococci, triplets, tetrads or small aggregates. After comparison of the complete 16S rRNA gene sequence, average amino-acid similarities and digital DNA-DNA hybridization values with that of the neighboring type species, we propose that the strain belongs to a novel genus and species, Ca. Methylolobus aquaticus FWC3Ts.

Enterococcus mundtii is a Gram-positive bacterium found in the environment and mammalian gastrointestinal tracts. It is also an infrequent cause of infections in humans. Here, we describe isolation, sequencing, and genomic analysis of four isolates of E. mundtii obtained from soil. These strains will be valuable tools for future work on understuded species of Enterococcus.

A Gram-positive, obligately anaerobic coccobacillus, with the white raised circular colony was isolated from the cecum of feral chickens in Brookings, South Dakota, USA. The 16S rRNA gene sequence analysis suggested that the closest species to strain SW178 was Ruminococcus torques ATCC 27756T (96.94% similarity) that belongs to the family Lachnospiraceae. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. Based on the phylogenetic and phenotypic comparison, we propose that strain SW178 be assigned to the genus Ruminococcus as a novel species, for which the name Ruminococcus catenae is proposed. The type strain is SW178 (= CCOS 1886 T, =DSM 109242T).

The emergence of the mobile resistance-nodulation-division (RND)-type efflux pump tmexCD-toprJ gene cluster that confers multidrug resistance (MDR), including tigecycline resistance, in gram-negative bacteria poses a global public health threat. However, the spread of such clinically important antimicrobial resistance genes (ARGs) in the natural environment has not yet been well investigated. In this study, we investigated MDR aquatic bacteria in Vietnam. A carbapenem- and tigecycline-resistant Shewanella xiamenensis isolate NUITM-VS2 was obtained from urban drainage in Hanoi, Vietnam, in October 2021. S. xiamenensis NUITM-VS2 showed resistance to most antimicrobials tested, including tigecycline, tetracyclines, carbapenems, cephalosporins, fluoroquinolone, and aminoglycosides. Whole-genome analysis was performed by long- and short-read sequencing, resulting in the complete genome sequence consisting of one chromosome and five plasmid sequences. ARGs and plasmid replicons in the genome were detected using ResFinder with the custom ARG database, including all known tigecycline resistance genes, and PlasmidFinder, respectively. A 152.2-kb IncC plasmid, pNUITM-VS2_2, co-carried two mobile tigecycline resistance genes, tet(X4) and tmexC3.2D3.2-toprJ1. In addition, a 24.8-kb untypeable plasmid, pNUITM-VS2_4, carried the carbapenemase gene blaNDM-1. pNUITM-VS2_2 was transferred to Escherichia coli by conjugation, which simultaneously conferred high-level resistance against many antimicrobials, including tigecycline. To the best of our knowledge, this is the first report of the detection of the mobile RND-type efflux pump gene cluster tmexCD-toprJ in Shewanella species. Our results provide genetic evidence of the complexity of the dynamics of clinically important ARGs among aquatic bacteria, which could be important reservoirs for ARGs in the natural environment.

Vibrio parahaemolyticus and Vibrio vulnificus are significant foodborne pathogens linked to seafood consumption and environmental exposure. Whole genome sequencing (WGS) was performed on Vibrio isolates collected from clinical cases and seafood sources throughout the state of New Jersey to elucidate genomic diversity, antimicrobial resistance (AMR) profiles. Sequences were included from isolates collected over eight years, from June 2016 to November 2024. This study identified 465 Vibrio sequences, 406 sequences from seafood sources and 59 sequences from clinical cases. Species-level taxonomic identification via Kraken2 classified 300 isolates as Vibrio parahaemolyticus and 165 as Vibrio vulnificus from whole genome assemblies. Multi-locus sequence typing (MLST) indicated a diverse population of isolates, with 169 known Vibrio sequence types (STs) identified. An additional 168 potential novel allelic profiles were identified, comprising 19.3% of V. parahaemolyticus sequences and 90.9% of V. vulnificus sequences. Novel sequence types were submitted to pubMLST for classification, resulting in the identification of 49 novel V. parahaemolyticus STs and 113 novel V. vulnificus STs. Three V. parahaemolyticus sequence types were identified in both clinical and environmental sequences. A single novel sequence type was identified in both clinical and environmental sequences of V. vulnificus. Analysis of antimicrobial resistance genes revealed the presence of the tetracycline resistance gene tet(34) in nearly all isolates. Beta-lactamase genes were detected in nearly all V. parahaemolyticus sequences but were absent from V. vulnificus, with gene profiles varying by sequence type. To the best of our knowledge, this study provides the first comprehensive WGS-based analysis of the genomic diversity and antimicrobial resistance profiles of Vibrio parahaemolyticus and Vibrio vulnificus isolates from clinical and seafood sources in New Jersey over an eight-year period, to support public health surveillance of these foodborne pathogens.

We present a genome assembly of Aiptasia strain F003, a broadly used laboratory strain of the sea anemone and coral model organism Exaiptasia diaphana (Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Aiptasiidae; Exaiptasia). The genome assembly spans 237.34 Mb across 12,480 contigs with a contig N50 of 76.47 kb (12,423 scaffolds with a scaffold N50 of 77.93 kb), including a single-contig mitochondrial genome with a length of 19.79 kb. The assembly is highly complete with a BUSCO completeness of 96.50% based on the metazoa dataset, including 94.80% single-copy, 1.70% duplicated, 1.70% fragmented, and 1.80% missing BUSCO genes. Genome annotation identified 29,589 protein-coding genes (including 2 pseudogenes) and a repeat content of 32.89%. The genome of the female Aiptasia strain F003 enhances the utility of a key cnidarian model organism by enabling comparisons among Aiptasia strains in studies of symbiosis, microbiomes, and thermal stress. It thereby strengthens the value of Aiptasia as a model for investigating the mechanisms underlying coral holobiont function, response, and resilience to environmental change.

SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.

A strictly anaerobic bacterial strain, F2T, was isolated from an anaerobic bioreactor fermenting source-separated organic waste. Cells of strain F2T are non-spore-forming, rod-shaped (1.5-2.5 x 0.27-0.33 m), and Gram-negative, although they possess a monoderm cell wall architecture. The strain grew at 37 degrees C within a pH range of 5 to 8 and produced short-, branched-, and medium-chain carboxylates as well as ammonium, H2 and CO2, with acetate and propanoate produced or consumed depending on fermentation conditions. The genome consists of a single 2.4 Mbp chromosome with a G+C content of 50.2% and 2,131 predicted genes. Phylogenetic analysis of the 16S rRNA gene against other isolates revealed that strain F2T is most similar to Eubacterium pyruvativorans I-6T (92.06% 16S rRNA identity). Based on further phenotypic, genomic, and phylogenetic analysis, strain F2T represents a novel genus and species within the family Anaerovoracaceae with the proposed name Peptonella octanoica gen. nov. sp. nov. The type strain is F2T (strain accession pending). As a member of this same genus-level clade, we propose reclassifying Eubacterium pyruvativorans as Peptonella pyruvativorans comb. nov. These findings disambiguate Peptonella spp. from the phylogenetically distant and phenotypically distinct Eubacterium limosum ATCC 8486T.

The genus Gardnerella comprises a group of fastidious bacteria associated with the female urogenital tract and has undergone extensive taxonomic revision in recent years. In this study, a bacterial strain, designated CCPDSM, was isolated from the female urinary microbiome and subjected to a comprehensive polyphasic taxonomic characterization. The 16S rRNA gene sequence confirmed that this strain is a member of the genus Gardnerella, and phylogenetic analyses based on cpn60 sequences, together with phylogenomic reconstruction placed strain CCPDSM within the genus Gardnerella as a distinct and well-supported lineage. Genome-based relatedness indices (ANIb, ANIm, TETRA and dDDH), demonstrated clear separation of CCPDSM from all validly published Gardnerella species. In contrast, comparisons with two publicly available closely related genomes yielded values above accepted species delineation thresholds, supporting their assignment to the same taxon. Phenotypic characterization, together with genome-based functional predictions, revealed a fastidious, fermentative metabolic profile that further differentiated CCPDSM from its closest relatives, while remaining consistent with traits characteristic of the genus. On the basis of combined phylogenetic, genomic and phenotypic evidence, strain CCPDSM is proposed as representing a novel species within the genus Gardnerella, for which the name Gardnerella fastidiominuta sp. nov. is proposed, with strain CCPDSM (=CECT 31324=CCP 588) designated as the type strain. This study expands the recognized diversity of Gardnerella and highlights the female urinary tract as a reservoir of previously uncharacterized species within this genus.