Marinococcus tarijensis sp. nov., a moderately halophilic bacterium isolated from a salt mine

A Multi-Omics Study of Familial Lung Cancer: Microbiome and Host Gene Expression Patterns

Background

Inherited susceptibility and environmental carcinogens are crucial players in lung cancer etiology. The lung microbiome is getting rising attention in carcinogenesis. The present work sought to investigate the microbiome in lung cancer patients affected by familial lung cancer (FLC) and indoor air pollution (IAP); and further, to compare host gene expression patterns with their microbiome for potential links.

Methods

Tissue sample pairs (cancer and adjacent nonmalignant tissue) were used for 16S rRNA (microbiome) and RNA-seq (host gene expression). Subgroup microbiome diversities and their matched gene expression patterns were analyzed. Significantly enriched taxa were screened out, based on different clinicopathologic characteristics.

Results

Our FLC microbiome seemed to be smaller, low-diversity, and inactive to change; we noted microbiome differences in gender, age, blood type, anatomy site, histology type, TNM stage as well as IAP and smoking conditions. We also found smoking and IAP dramatically decreased specific-OTU biodiversity, especially in normal lung tissue. Intriguingly, enriched microbes were in three categories: opportunistic pathogens, probiotics, and pollutant-detoxication microbes; this third category involved Sphingomonas, Sphingopyxis, etc. which help degrade pollutants, but may also cause epithelial damage and chronic inflammation. RNA-seq highlighted IL17, Ras, MAPK, and Notch pathways, which are associated with carcinogenesis and compromised immune system.

Conclusions

The lung microbiome can play vital roles in carcinogenesis. FLC and IAP subjects were affected by fragile lung epithelium, vulnerable host-microbes equilibrium, and dysregulated immune surveillance and response. Our findings provided useful information to study the triple interplay among environmental carcinogens, population genetic background, and diversified lung microbiome.

Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh

A novel Gram-stain-positive, coccoid-shaped, facultative anaerobic, motile and halophilic bacterium strain 5M^T was isolated from Surajbari in India. Based on the 16S rRNA gene sequence analysis, it was identified as belonging to the genus Marinococcus and was most closely related to Marinococcus luteus KCTC 13214^T (99.3 %, sequence similarity), Marinococcus halotolerans KCTC 19045^T (99.0 %), Marinococcus halophilus LMG 17439^T (98.8 %) and Marinococcus tarijensis LMG 26930^T (98.7 %). However, the DNA-DNA relatedness of strain 5M^T with M. luteus KCTC 13214^T, M. halotolerans KCTC 19045^T, M. halophilus LMG 17439^T and M. tarijensis LMG 26930^T was 42.6 ± 0.8, 48.6 ± 0.8, 40.9 ± 0.8 and 39.8 ± 0.9 %, respectively. Strain 5M^T grows optimally at 5 % (w/v) NaCl, pH 7.5-8.5 and 37 °C. The cell-wall peptidoglycan of strain 5M^T contains meso-diaminopimelic acid. Polar lipids of the strain 5M^T include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and two unknown lipids. The predominant isoprenoid quinone was MK-7. DNA G+C content was 48.9 mol%, and anteiso-C_15:0 (40.9 %) was the predominant fatty acid. The results of phylogenetic, biochemical tests and chemotaxonomic allowed a clear differentiation of strain 5M^T from all of its nearest phylogenetic neighbours, which represents a novel member of the genus Marinococcus, for which the name Marinococcus salis sp., nov., is proposed. The type strain is 5M^T (=KCTC 33743^T = LMG 29101^T = CGMCC 1.15385^T).

Halophilic microorganisms are responsible for the rosy discolouration of saline environments in three historical buildings with mural paintings

A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.