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Lignin-derived aromatic compounds have significant potential for multiple industrial applications, and elucidating the processes for bacterial lignin degradation processes can facilitate the utilization of plant biomass. A lignin-degrading bacterial strain, designated HZC-1, was newly isolated from saline-alkali soil and exhibited robust growth in 1–18% (w/v) NaCl and across a pH range of 5.0–11.0. The isolate showed the highest 16S rRNA gene sequence similarity (≤ 97.7%) to known Salinicoccus species. Furthermore, average nucleotide identity (≤ 82.34) and digital DNA-DNA hybridization (≤ 52.9%) analyses supported its classification as a potentially novel species within the genus Salinicoccus . Genomic annotation indicated that strain HZC-1 adapted to saline-alkali environments via multiple mechanisms such as Na + /H + antiporter and glycine betaine transport systems. By combining genomic and untargeted metabolomic data, it can be inferred that this strain was capable of metabolizing lignin derivatives through non-classical pathways involving enzymes such as β-glucosidase, aromatic cyclohydroxyl dioxygenase and those associated with naphthalene degradation. These findings suggest the potential lignin-degrading capacity of Salinicoccus sp. HZC-1 under saline-alkali conditions, presenting a potentially novel bacterial taxon for waste lignin valorization and bioremediation of aromatic pollutants.

Virus host shifts, where a virus transmits to and infects a novel host species, are a major source of emerging infectious disease. Genetic similarity between eukaryotic host species has been shown to be an important determinant of the outcome of virus host shifts, but it is unclear if this is the case for prokaryotes where anti-virus defences can be transmitted by horizontal gene transfer and evolve rapidly. Here, we measure the susceptibility of 64 strains of Staphylococcaceae bacteria (48 strains of Staphylococcus aureus and 16 non- S . aureus species spanning 2 genera) to the bacteriophage ISP, which is currently under investigation for use in phage therapy. Using three methods–plaque assays, optical density (OD) assays, and quantitative (q)PCR–we find that the host phylogeny explains a large proportion of the variation in susceptibility to ISP across the host panel. These patterns were consistent in models of only S . aureus strains and models with a single representative from each Staphylococcaceae species, suggesting that these phylogenetic effects are conserved both within and among host species. We find positive correlations between susceptibility assessed using OD and qPCR and variable correlations between plaque assays and either OD or qPCR, suggesting that plaque assays alone may be inadequate to assess host range. Furthermore, we demonstrate that the phylogenetic relationships between bacterial hosts can generally be used to predict the susceptibility of bacterial strains to phage infection when the susceptibility of closely related hosts is known, although this approach produced large prediction errors in multiple strains where phylogeny was uninformative. Together, our results demonstrate the ability of bacterial host evolutionary relatedness to explain differences in susceptibility to phage infection, with implications for the development of ISP both as a phage therapy treatment and as an experimental system for the study of virus host shifts.

In the context of increasingly airtight homes, there is currently little known about the type and diversity of microorganisms in the home, or factors that could affect their abundance, diversity and nature. In this study, we examined the type and prevalence of cultivable microorganisms at eight different sites in 100 homes of older adults located in Glasgow, Scotland. The microbiological sampling was undertaken alongside a household survey that collated information on household demographics, occupant behaviour, building characteristics, antibiotic use and general health information. Each of the sampled sites revealed its own distinct microbiological character, in both species and number of cultivable microbes. While some potential human pathogens were identified, none were found to be multidrug resistant. We examined whether the variability in bacterial communities could be attributed to differences in building characteristics, occupant behaviour or household factors. Sampled sites furnished specific microbiological characteristics which reflected room function and touch frequency. We found that homes that reported opening windows more often were strongly associated with lower numbers of Gram-negative organisms at indoor sites (p < 0.0001). This work offers one of the first detailed analysis of cultivable microbes in homes of older adults and their relationship with building and occupancy related factors, in a UK context.

Introduction: Neonatal sepsis, a clinical syndrome characterized by systemic signs of infection in newborn infants (< 28 days old), are a significant cause of neonatal mortality and long-term morbidity globally, particularly in low- and middle- income countries. Case presentation: We report the first case of neonatal sepsis caused by Macrococcus caseolyticus in a 48-hours old newborn who attended to the intensive care unit (ICU) of the Kassala Specialized Hospital for Pediatrics in Sudan, with signs of severe bacterial infection. M. caseolyticus is an opportunistic pathogen normally associated with veterinary and food-borne infections. Empirical antibiotic therapy was promptly initiated following blood sampling and culture, resulting in recovery within 4 days. M. caseolyticus was identified by mass spectrometry and confirmed by whole genome sequencing. The isolated strain, KaM20, was resistant to tetracycline, due to the presence of the tet(L) gene; and harbored several virulence-associated genes. Phylogenetic analysis including M. caseolyticus genomes from the GenBank suggested an animal origin for KaM20. Conclusions: This case presents a rare instance of neonatal sepsis caused by M. caseolyticus; indicating potential zoonotic transmission of this pathogen, through maternal or environmental exposure to animals in the rural household. The findings emphasize the need for increased awareness of zoonotic infections in neonatal care, particularly in regions where exposure to animals is common; and underscore the importance of understanding the complex interplay between host factors, environmental exposures, and microbial pathogens, in the development of neonatal sepsis; reinforcing the need of a 'One Health' approach in addressing emerging infectious diseases.

Background While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung’s bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information on bacterial function and impact on the host. Metabolic profiles can provide functional information on host-microbe interactions in the lungs. We investigated the relationship between the respiratory microbiota and metabolic profiles in the bronchoalveolar lavage fluid of HIV-infected and HIV-uninfected outpatients. Results Targeted sequencing of the 16S rRNA gene was used to analyze the bacterial community structure and liquid chromatography-high-resolution mass spectrometry was used to detect features in bronchoalveolar lavage fluid. Global integration of all metabolic features with microbial species was done using sparse partial least squares regression. Thirty-nine HIV-infected subjects and 20 HIV-uninfected controls without acute respiratory symptoms were enrolled. Twelve mass-to-charge ratio ( m/z) features from C18 analysis were significantly different between HIV-infected individuals and controls (false discovery rate (FDR) = 0.2); another 79 features were identified by network analysis. Further metabolite analysis demonstrated that four features were significantly overrepresented in the bronchoalveolar lavage (BAL) fluid of HIV-infected individuals compared to HIV-uninfected, including cystine, two complex carbohydrates, and 3,5-dibromo- l -tyrosine. There were 231  m/z features significantly associated with peripheral blood CD4 cell counts identified using sparse partial least squares regression (sPLS) at a variable importance on projection (VIP) threshold of 2. Twenty-five percent of these 91  m/z features were associated with various microbial species. Bacteria from families Caulobacteraceae , Staphylococcaceae , Nocardioidaceae , and genus Streptococcus were associated with the greatest number of features. Glycerophospholipid and lineolate pathways correlated with these bacteria. Conclusions In bronchoalveolar lavage fluid, specific metabolic profiles correlated with bacterial organisms known to play a role in the pathogenesis of pneumonia in HIV-infected individuals. These findings suggest that microbial communities and their interactions with the host may have functional metabolic impact in the lung.

Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2-3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.

Symbionts are widely distributed in eukaryotes, and potentially affect the physiology, ecology and evolution of their host. Most insects harbour free-living bacteria in their haemocoel and gut lumen, intracellular-living bacteria in a range of tissues or bacteria in host-derived specialized cells. Stinkbugs, as do many arthropods, harbour extracellular bacteria in the gut that may affect the fitness of their host. This study identified the culturable symbionts associated with the ovaries, spermatheca, seminal vesicle and posterior midgut region (V4) of males and females of Euschistus heros (F.) (Hemiptera: Pentatomidae). Several culture media were used to isolate the bacteria associated with these structures. The selected colonies (morphotypes) were cultured in liquid medium, subjected to genomic DNA extraction, 16S rRNA gene amplification, and restriction fragment length polymorphism (RFLP) analyses. Morphotypes with distinct RFLP patterns were purified and sequenced, and the sequences obtained were used for putative identification and phylogenetic analysis. Comparison of the sequences with those available in the EzTaxon-e database and the use of a matrix of paired distances grouped the isolates in phylotypes belonging to the Phylum Proteobacteria. Proteobacteria was represented by γ-Proteobacteria phylotypes belonging to Enterobacteriaceae, while Firmicutes had Bacilli phylotypes distributed in Enterococcaceae and Staphylococcaceae. Some of the phylotypes identified were associated exclusively with single structures, such as ovaries, spermatheca and the V4 midgut region of males and females. All culturable bacteria associated with the seminal vesicle were also associated with other tissues.

A Gram-stain positive, aerobic, non-motile, asporogenous, coccoid shaped bacterium, designated YIM M12140 T , was isolated from a marine sediment sample collected from the Indian Ocean. Phylogenetic analysis showed that strain YIM M12140 T forms a separate clade within the family Staphylococcaceae . Strain YIM M12140 T shares high 16S rRNA gene sequence similarity with Macrococcus brunensis DSM 19358 T (92.9 %). The isolate was found to grow at 0–10 % (w/v) NaCl (optimum, 2–3 %), pH 6.0–10.0 (optimum, pH 8.0) and temperature 5–40 °C (optimum, 28 °C). The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid and two unidentified polar lipids. The major cellular fatty acids of the strain were identified as anteiso-C 15:0 , -C 17:0 , iso-C 16:0 , anteiso-C 19:0 and C 20:0 . The respiratory menaquinones were found to be MK-6 (94 %) and MK-7 (6 %). The cell wall amino acids were found to contain Lys, Ala, Glu, Gly, Asp, Ser and Thr. Whole cell sugars were identified as mannose, ribose, rhamnose, glucose, galactose and xylose. The G+C content of the genomic DNA of strain YIM M12140 T was determined to be 42.4 mol %. Based on phenotypic, chemotaxonomic data and phylogenetic analysis, it is proposed that strain YIM M12140 T represents a novel species of a new genus in the family Staphylococcaceae , for which the name Abyssicoccus albus gen. nov., sp. nov. is proposed. The type strain is YIM M12140 T (= DSM 29158 T  = CCTCC AB 2014213 T ).

Strain JC90 T was isolated from a soda lake in Lonar, India. Strain JC90 T maintains its external pH to 8.5 and participates in halite formation. Based on 16S rRNA gene sequence similarity studies, strain JC90 T was found to belong to the genus Salinicoccus and is most closely related to “ Salinicoccus kekensis ” K164 T (99.3 %), Salinicoccus alkaliphilus T8 T (98.4 %) and other members of the genus Salinicoccus (<96.5 %). However Strain JC90 T is <36 % related (based on DNA–DNA hybridization) with the type strains of “ S . kekensis ” K164 T and S. alkaliphilus T8 T . The DNA G+C content of strain JC90 T was determined to be 46 mol %. The cell-wall amino acids were identified as lysine and glycine. Polar lipids were found to include diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl ethanolamine, an unidentified glycolipid and unidentified lipids (L1,2). Major hopanoids of strain JC90 T were determined to be bacterial hopane derivatives (BHD1,2), diplopterol, diploptene and two unidentified hopanoids (UH1,2). The predominant isoprenoid quinone was identified as menaquinone (MK-6). Anteiso -C 15:0 was determined to be the predominant fatty acid and significant proportions of iso -C 14:0 , C 14:0 , iso -C 15:0 , C 16:0 , iso -C 16:0 , iso -C 17:0 , anteiso -C 17:0 and C 18:0 2OH were also detected. The results of physiological and biochemical tests support the molecular evidence and allowed a clear phenotypic differentiation of strain JC90 T from all other members of the genus Salinicoccus . Strain JC90 T is therefore considered to represent a novel species, for which the name Salinicoccus halitifaciens sp. nov. is proposed. The type strain is JC90 T (=KCTC 13894 T =DSM 25286 T ).

A novel alkaliphilic and moderate halophilic bacterium, designated strain K164 T , was isolated from Keke Salt Lake in Qinghai, China. The strain grew with 2.0–20.0% (w/v) NaCl, at 4–50°C and pH 6.5–11.5, with an optimum of 8% (w/v) NaCl, 37°C and pH 10, respectively. The predominant respiratory quinone was menaquinone 6 (MK-6) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were anteiso-C 15:0 and iso-C 15:0 . The genomic DNA G+C content was 50.16 mol. Phylogenetic analysis based on the full-length 16S rRNA gene sequence revealed that strain K164 T was a member of the genus Salinicoccus . Strain K164 T showed the highest similarity (98.4%) with Salinicoccus alkaliphilus AS 1.2691 T and below 97% similarity with other recognized members of the genus in 16S rRNA gene sequence. Level of DNA–DNA relatedness between strain K164 T and Salinicoccus alkaliphilus AS 1.2691 T was 20.1%. On the basis of its phenotypic characteristics and the level of DNA–DNA hybridization, strain K164 T is considered to represent a novel species of the genus Salinicoccus , for which the name Salinicoccus kekensis sp. nov. is proposed. The type strain is K164 T (=CGMCC 1.10337 T  = DSM 23173 T ).