Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits.

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.

Metagenome-assembled genomes from particle-associated microbial communities in the mesopelagic zone of the Pacific Ocean.

We report 10 particle-associated metagenome-assembled genomes (MAGs) from the mesopelagic zone of Pacific Ocean seawaters. MAGs comprise members of Flavobacteria Halomonas, Blastomonas, Brevundimonas, Alteromonas, Shingomonas, Sphingopyxis, Tabrizicola, Proteobacteria, and Gammaproteobacteria. Functional annotation suggests that these bacteria are involved in central particulate organic carbon conversion, nitrogen cycling, and phosphorus cycling.

Complete Genome Sequence of Citrobacter braakii GW-Imi-1b1, Isolated from Hospital Wastewater in Greifswald, Germany.

The imipenem-resistant Citrobacter braakii strain GW-Imi-1b1 was isolated from a hospital wastewater sample in Greifswald, Germany. The genome comprises one chromosome (5.09 Mb), one prophage (41.9 kb), and 13 plasmids (2 to 140.9 kb). The genome harbors 5,322 coding sequences, shows a high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances.

Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies.

Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and the generation of cDNA from the isolated RNA that can be used as a universal template in various marker gene studies.

Biofilm formation and inflammatory potential of Staphylococcus saccharolyticus: A possible cause of orthopedic implant-associated infections.

Staphylococcus saccharolyticus, a coagulase-negative staphylococcal species, has some unusual characteristics for human-associated staphylococci, such as slow growth and its preference for anoxic culture conditions. This species is a relatively abundant member of the human skin microbiota, but its microbiological properties, as well as the pathogenic potential, have scarcely been investigated so far, despite being occasionally isolated from different types of infections including orthopedic implant-associated infections. Here, we investigated the growth and biofilm properties of clinical isolates of S. saccharolyticus and determined host cell responses. Growth assessments in anoxic and oxic conditions revealed strain-dependent outcomes, as some strains can also grow aerobically. All tested strains of S. saccharolyticus were able to form biofilm in a microtiter plate assay. Strain-dependent differences were determined by optical coherence tomography, revealing that medium supplementation with glucose and sodium chloride enhanced biofilm formation. Visualization of the biofilm by confocal laser scanning microscopy revealed the role of extracellular DNA in the biofilm structure. In addition to attached biofilms, S. saccharolyticus also formed bacterial aggregates at an early stage of growth. Transcriptome analysis of biofilm-grown versus planktonic cells revealed a set of upregulated genes in biofilm-embedded cells, including factors involved in adhesion, colonization, and competition such as epidermin, type I toxin-antitoxin system, and phenol-soluble modulins (beta and epsilon). To investigate consequences for the host after encountering S. saccharolyticus, cytokine profiling and host cell viability were assessed by infection experiments with differentiated THP-1 cells. The microorganism strongly triggered the secretion of the tested pro-inflammatory cyto- and chemokines IL-6, IL-8, and TNF-alpha, determined at 24 h post-infection. S. saccharolyticus was less cytotoxic than Staphylococcus aureus. Taken together, the results indicate that S. saccharolyticus has substantial pathogenic potential. Thus, it can be a potential cause of orthopedic implant-associated infections and other types of deep-seated infections.

Complete Genome Sequence of the Type Strain Aliivibrio fischeri DSM 507.

The complete genome sequence of the type strain Aliivibrio fischeri comb. nov. DSM 507 is presented. The genome consists of two circular chromosomes comprising 2,970,859 bp (chromosome 1) and 1,532,347 bp (chromosome 2) with GC contents of 38.94 and 37.13%, respectively.

Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica.

A Gram-negative bacterial strain, G163CMT, was isolated from the gut of the Asian emerald cockroach Corydidarum magnifica. The 16S rRNA gene sequence (1416 bp) of strain G163CMT showed 99.22% similarity to Pseudocitrobacter faecalis CCM 8479T and Pseudocitrobacter vendiensis CPO20170097T. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values of strain G163CMT were 92.4, 48.8 and 95.7% to P. faecalis CCM 8479T, and 93.3, 52.4 and 95.7% to P. vendiensis CPO20170097T. This strongly supports the designation of G163CMT as representing a new species in the genus Pseudocitrobacter. Phylogenetic trees based on the alignment of 16S rRNA, multilocus sequence analysis of six single-copy genes (fusA, pyrG, leuS, rpoB, recN and mnmE) and 107 core protein sequences consistently showed G163CMT to be a member of the genus Pseudocitrobacter, closely related to P. vendiensis CPO20170097T. In contrast to P. faecalis CCM 8479T and P. vendiensis CPO20170097T, the genome of G163CMT did not encode for proteins conferring resistance to antibiotics. However, all three genomes encoded a similar number of virulence factors and specialized metabolite biosynthetic proteins. The major fatty acids of strain G163CMT were C16:0 (31.5 %), C18:1 ω7c (22.6 %), C17:0 cyclo (15.3 %) and C14:0 (6.5 %). Based on the polyphasic results, we conclude that strain G163CMT represents a novel species of the genus Pseudocitrobacter and we propose the name Pseudocitrobacter corydidari sp. nov. with the type strain G163CMT (=DSM 112648T=CCM 9160T).

Complete Genome Sequence of Bacillus frigoritolerans JHS1.

Bacillus frigoritolerans JHS1 was isolated from the soil of a tomato plant (Solanum lycopersicum). The genome consists of one circular chromosome (5,552,463 bp) and a plasmid (16,118 bp) with an overall GC content of 40.57%. Using TYGS for taxonomic classification, strain JHS1 was assigned to the species Bacillus frigoritolerans.

The lung microbiome regulates brain autoimmunity.

Lung infections and smoking are risk factors for multiple sclerosis, a T-cell-mediated autoimmune disease of the central nervous system1. In addition, the lung serves as a niche for the disease-inducing T cells for long-term survival and for maturation into migration-competent effector T cells2. Why the lung tissue in particular has such an important role in an autoimmune disease of the brain is not yet known. Here we detected a tight interconnection between the lung microbiota and the immune reactivity of the brain. A dysregulation in the lung microbiome significantly influenced the susceptibility of rats to developing autoimmune disease of the central nervous system. Shifting the microbiota towards lipopolysaccharide-enriched phyla by local treatment with neomycin induced a type-I-interferon-primed state in brain-resident microglial cells. Their responsiveness towards autoimmune-dominated stimulation by type II interferons was impaired, which led to decreased proinflammatory response, immune cell recruitment and clinical signs. Suppressing lipopolysaccharide-producing lung phyla with polymyxin B led to disease aggravation, whereas addition of lipopolysaccharide-enriched phyla or lipopolysaccharide recapitulated the neomycin effect. Our data demonstrate the existence of a lung-brain axis in which the pulmonary microbiome regulates the immune reactivity of the central nervous tissue and thereby influences its susceptibility to autoimmune disease development.

Complete Genome Sequence of Kinneretia sp. Strain DAIF2, Isolated from a Freshwater Pond.

Kinneretia sp. strain DAIF2 was isolated from a eutrophic freshwater pond. The genome consists of a single chromosome (6,010,585 bp) with a GC content of 69.3%. The whole-genome-based phylogeny of DAIF2 revealed a closest relation to the genus Kinneretia.

Complete Genome Sequence of Stenotrophomonas indicatrix DAIF1.

We present the complete genome of Stenotrophomonas indicatrix DAIF1, which was isolated from an oligotrophic pond in a water protection area. Whole-genome alignments indicated that strain DAIF1 belongs to the species Stenotrophomonas indicatrix The whole genome (4,639,375 bp) harbors 4,108 protein-encoding genes, including 3,029 genes with assigned functions.

First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and Their Comparative Genome Analysis.

We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in Göttingen. The strains were phylogenetically classified by average nucleotide identity (ANI) analysis and showed a species assignment to J. lividum with 97.72% (EIF1) and 97.66% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species J. lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a nonribosomal peptide synthetase cluster with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites.

Complete Genome of Roseobacter ponti DSM 106830T.

Members of the Roseobacter group are known for their different ecologically relevant metabolic traits and high abundance in many marine environments. This includes traits like carbon monoxide oxidation, sulfur oxidation, nitrogen oxidation, DMSP demethylation, denitrification, and production of bioactive compounds. Nevertheless, their role in the marine biogeochemical cycles remains to be elucidated. Roseobacter ponti DSM 106830T, also designated strain MM-7T (=KCTC 52469T =NBRC 112431T), is a novel type strain of the Roseobacter group, which was proposed as new Roseobacter species. It was isolated from seawater of the Yellow Sea in South Korea. We report the complete genome sequence of R. ponti DSM 106830T, which belongs to the family Rhodobacteraceae. The genome of R. ponti DSM 106830T comprises a single circular chromosome (3,861,689 bp) with a GC content of 60.52% and an additional circular plasmid (p1) of 100,942 bp with a GC content of 61.51%. The genome encodes 3,812 putative genes, including 3 rRNA, 42 tRNA, 1 tmRNA, and 3 ncRNA. The genome information was used to perform a phylogenetic analysis, which confirmed that the strain represents a new species. Moreover, the genome sequence enabled the investigation of the metabolic capabilities and versatility of R. ponti DSM 106830T. Finally, it provided insight into the high niche adaptation potential of Roseobacter group members.

Genome Sequence of Komagataeibacter saccharivorans Strain JH1, Isolated from Fruit Flies.

We present the genome sequence of Komagataeibacter saccharivorans strain JH1, which belongs to the acetic acid bacteria. The draft genome sequence consists of 3.7 Mb and contains 3,437 predicted protein-encoding genes. This organism contains putative genes involved in cellulose and levan biosynthesis.

Complete Genome Sequence of Sporomusa termitida DSM 4440T.

Sporomusa termitida type strain DSM 4440 was isolated from the intestinal content of the termite Nasutitermes nigriceps The genome consists of one circular chromosome (5,185,220 bp) and a megaplasmid (131,121 bp) with an overall G+C content of 49.11%. It harbors 4,764 predicted protein-encoding genes.

Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord.

Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes.

Draft Genome Sequence of Komagataeibacter maltaceti LMG 1529T, a Vinegar-Producing Acetic Acid Bacterium Isolated from Malt Vinegar Brewery Acetifiers.

We present the genome sequence of Komagataeibacter maltaceti LMG 1529T, which is a vinegar-producing acetic acid bacterium. The draft genome sequence consists of 3.6 Mb and contains 3,225 predicted protein-encoding genes. In addition, 53 genes encoding potential oxidoreductases were identified.

Draft Genome Sequence of the Endophyte Paenibacillus sp. Strain GM2FR Isolated from Festuca rubra.

Here, we report the 7.4-Mb draft genome sequence of Paenibacillus sp. strain GM2FR, an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Genome analysis revealed 6,652 coding gene sequences and several gene clusters involved in plant growth promotion, such as that for the siderophore bacillibactin.

Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM6LP Isolated from Lolium perenne.

Bacillus mycoides GM6LP is an endophyte isolated from plant tissues of Lolium perenne L. Here, we report its draft genome sequence (6.2 Mb), which contains 96 contigs and 6,129 protein-coding genes. Knowledge about its genome will enable us to evaluate the potential use of GM6LP as a plant growth-promoting bacterium.

First Insights into the Draft Genome Sequence of the Endophyte Paenibacillus amylolyticus Strain GM1FR, Isolated from Festuca rubra L.

Paenibacillus amylolyticus strain GM1FR is an endophyte isolated from aerial plant tissues of Festuca rubra L. Here, we report the draft genome sequence (7.3 Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially involved in plant growth promotion and biocontrol.