Authors: K Leigh Greathouse, James R White, Ashely J Vargas...

BACKGROUND

Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort.

RESULTS

Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas.

CONCLUSIONS

The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.

Topics: Adult; Aged; Biodiversity; Comamonadaceae; Female; Humans; Lung Neoplasms; Male; Microbiota; Middle Aged; Mutation; Neoplasms, Squamous Cell; Proteobacteria; Reproducibility of Results; Smokers; Tumor Suppressor Protein p53

PubMed: 30143034
DOI: 10.1186/s13059-018-1501-6

Authors: Rosario Palacio, Cecilia Cornejo, Verónica Seija...

Topics: Bacterial Typing Techniques; Comamonas; DNA, Bacterial

PubMed: 32730480
DOI: 10.4067/s0716-10182020000200147

Authors: Thiruselvam Viswanathan, Jian Chen, Minghan Wu...

The ant operon of the antimony-mining bacterium Comamonas testosterone JL40 confers resistance to Sb(III). The operon is transcriptionally regulated by the product of the first gene in the operon, antR. AntR is a member of ArsR/SmtB family of metal/metalloid-responsive repressors resistance. We purified and characterized C. testosterone AntR and demonstrated that it responds to metalloids in the order Sb(III) = methylarsenite (MAs(III) >> As(III)). The protein was crystallized, and the structure was solved at 2.1 Å resolution. The homodimeric structure of AntR adopts a classical ArsR/SmtB topology architecture. The protein has five cysteine residues, of which Cys103 from one monomer and Cys113 from the other monomer, are proposed to form one Sb(III) binding site, and Cys113 and Cys103 forming a second binding site. This is the first report of the structure and binding properties of a transcriptional repressor with high selectivity for environmental antimony.

Topics: Amino Acid Sequence; Antimony; Arsenic; Arsenicals; Binding Sites; Comamonas testosteroni; Gene Expression Regulation, Bacterial; Protein Conformation; Repressor Proteins; Transcription Factors; Transcription, Genetic

PubMed: 33786926
DOI: 10.1111/mmi.14721

Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis.

Authors: Fruzsina Révész, Milán Farkas, Balázs Kriszt...

The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.

Topics: Benzene; Benzene Derivatives; Biodegradation, Environmental; Comamonadaceae; Oxygen; Pseudomonas; Toluene; Xylenes

PubMed: 32474783
DOI: 10.1007/s11356-020-09277-z

Authors: Lijin An, Xiong Luo, Minghan Wu...

Antimony, like arsenic, is a toxic metalloid widely distributed in the environment. Microbial detoxification of antimony has recently been identified. Here we describe a novel bacterial P-type antimonite (Sb(III))-translocating ATPase from the antimony-mining bacterium Comamonas testosterone JL40 that confers resistance to Sb(III). In a comparative proteomics analysis of strain JL40, an operon (ant operon) was up-regulated by Sb(III). The ant operon includes three genes, antR, antC and antA. AntR belongs to the ArsR/SmtB family of metalloregulatory proteins that regulates expression of the ant operon. AntA belongs to the P family of the P-type cation-translocating ATPases. It has both similarities to and differences from other members of the P subfamily and appears to be the first identified member of a distinct subfamily that we designate P. Expression AntA in E. coli AW3110 (Δars) conferred resistance to Sb(III) and reduced the intracellular concentration of Sb(III) but not As(III) or other metals. Everted membrane vesicles from cells expressing antA accumulated Sb(III) but not As(III), where uptake in everted vesicles reflects efflux from cells. AntC is a small protein with a potential Sb(III) binding site, and co-expression of AntC with AntA increased resistance to Sb(III). We propose that AntC functions as an Sb(III) chaperone to AntA, augmenting Sb(III) efflux. The identification of a novel Sb(III)-translocating ATPase enhances our understanding of the biogeochemical cycling of environmental antimony by bacteria.

Topics: Adenosine Triphosphatases; Antimony; Comamonas testosteroni; Escherichia coli; P-type ATPases

PubMed: 33254899
DOI: 10.1016/j.scitotenv.2020.142393

Authors: Hiroshi Habe, Yuya Sato, Toshiaki Taira...

A total of 100 environmental samples were investigated for their ability to degrade 1 g/L surfactin as a substrate. Among them, two enrichment cultures, which exhibited microbial growth as well as surfactin degradation, were selected and further investigated. After several successive cultivations, nanopore sequencing of full-length 16S rRNA genes with MinION was used to analyze the bacterial species in the enrichment cultures. Variovorax spp., Caulobacter spp., Sphingopyxis spp., and Pseudomonas spp. were found to be dominant in these surfactin-degrading mixed cultures. Finally, one strain of Pseudomonas putida was isolated as a surfactin-degrading bacterium. This strain degraded 1 g/L surfactin below a detectable level within 14 days, and C surfactin was degraded faster than C surfactin.

Topics: Biodegradation, Environmental; Caulobacter; Comamonadaceae; Lipopeptides; Peptides, Cyclic; Pseudomonas putida; Sphingomonadaceae; Surface-Active Agents

PubMed: 33692244
DOI: 10.5650/jos.ess20331

Authors: Chae Yung Woo, Jaisoo Kim

A white-pigmented, non-motile, gram-negative, and rod-shaped bacterium, designated CYS-02, was isolated from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20-28ºC and hydrolyzed Tween 40. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CYS-02 formed a lineage within the family and clustered as members of the genus . The closest members were DSM 27352 (98.6% sequence similarity), NBRC 15149 (98.5%), and JM-310 (98.3%). The principal respiratory quinone was Q-8 and the major polar lipids contain phosphatidylethanolamine (PE), phosphatidylethanolamine (PG), and diphosphatidylglycerol (DPG). The predominant cellular fatty acids were C, summed feature 3 (C7c and/or C6c) and summed feature 8 (C7c and/or C6c). The DNA GC content was 67.7 mol%. The ANI and dDDH values between strain CYS-02 and the closest members in the genus were ≤ 79.0 and 22.4%, respectively, and the AAI and POCP values between CYS-02 and the other related species in the family were > 70% and > 50%, respectively. The genome of strain CYS-02 showed a putative terpene biosynthetic cluster responsible for antioxidant activity which was supported by DPPH radical scavenging activity test. Based on genomic, phenotypic and chemotaxonomic analyses, strain CYS-02 was classified into a novel species in the genus , for which the name sp. nov., has been proposed. The type strain is CYS-02 (= KACC 22656 = NBRC 115645 [corrected] ).

Topics: Antioxidants; Bacterial Typing Techniques; Comamonadaceae; DNA, Bacterial; Fatty Acids; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Soil Microbiology

PubMed: 35791077
DOI: 10.4014/jmb.2205.05018

Review

Authors: Yun-Hao Wang, Zhou Huang, Shuang-Jiang Liu...

Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in . Other representative bacteria, such as , species, , and , also have been deeply studied and systemically summarized. These bacteria belong to α-, γ-, ε-Proteobacteria, or Firmicutes. However, β-Proteobacteria, of which many members have been identified as holding chemotactic pathways, lack a summary of chemotaxis. , belonging to β-Proteobacteria, grows with and chemotactically responds to a range of aromatic compounds. This paper summarizes the latest research on chemotaxis towards aromatic compounds, mainly from investigations of and other species.

Topics: Bacterial Proteins; Chemotaxis; Comamonas testosteroni; Computational Biology; Genome, Bacterial; Genomics; Gram-Negative Bacterial Infections; Humans; Hydrocarbons, Aromatic; Signal Transduction

PubMed: 31159416
DOI: 10.3390/ijms20112701

Review

Authors: Alexandre Ranc, Grégory Dubourg, Pierre Edouard Fournier...

Delftia tsuruhatensis, which was first isolated in environmental samples, was rarely associated with human infections. We report on pneumonia caused by D. tsuruhatensis in an infant who underwent cardiac surgery. Retrospective analyses detected 9 other isolates from 8 patients. D. tsuruhatensis is an emergent pathogen, at least for immunocompromised patients.

Topics: Communicable Diseases, Emerging; Cross Infection; Delftia; France; Gram-Negative Bacterial Infections; Humans; Infant; Opportunistic Infections

PubMed: 29460754
DOI: 10.3201/eid2403.160939

Authors: Zhi-Jing Xu, Jim C Spain, Ning-Yi Zhou...

Halonitrobenzenes are toxic chemical intermediates used widely for industrial synthesis of dyes and pesticides. Bacteria able to degrade 2- and 4-chloronitrobenzene have been isolated and characterized; in contrast, no natural isolate has been reported to degrade -halonitrobenzenes. In this study, sp. strain JS3051, previously reported to degrade 2,3-dichloronitrobenzene, grew readily on 3-chloronitrobenzene and 3-bromonitrobenzene, but not on 3-fluoronitrobenzene, as sole sources of carbon, nitrogen, and energy. A Rieske nonheme iron dioxygenase (DcbAaAbAcAd) catalyzed the dihydroxylation of 3-chloronitrobenzene and 3-bromonitrobenzene, resulting in the regiospecific production of ring-cleavage intermediates 4-chlorocatechol and 4-bromocatechol. The lower activity and relaxed regiospecificity of DcbAaAbAcAd toward 3-fluoronitrobenzene is likely due to the higher electronegativity of the fluorine atom, which hinders it from interacting with E204 residue at the active site. DccA, a chlorocatechol 1,2-dioxygenase, converts 4-chlorocatechol and 4-bromocatechol into the corresponding halomuconic acids with high catalytic efficiency, but with much lower / values for fluorocatechol analogues. The results indicate that the Dcb and Dcc enzymes of sp. strain JS3051 can catalyze the degradation of 3-chloro- and 3-bromonitrobenzene in addition to 2,3-dichloronitrobenzene. The ability to utilize multiple substrates would provide a strong selective advantage in a habitat contaminated with mixtures of chloronitrobenzenes. Halonitroaromatic compounds are persistent environmental contaminants, and some of them have been demonstrated to be degraded by bacteria. Natural isolates that degrade 3-chloronitrobenzene and 3-bromonitrobenzene have not been reported. In this study, we report that sp. strain JS3051 can degrade 2,3-dichloronitrobenzene, 3-chloronitrobenzene, and 3-bromonitrobenzene using the same catabolic pathway, whereas it is unable to grow on 3-fluoronitrobenzene. Based on biochemical analyses, it can be concluded that the initial dioxygenase and lower pathway enzymes are inefficient for 3-fluoronitrobenzene and even misroute the intermediates, which is likely responsible for the failure to grow. These results advance our understanding of how the broad substrate specificities of catabolic enzymes allow bacteria to adapt to habitats with mixtures of xenobiotic contaminants.

Topics: Biodegradation, Environmental; Comamonadaceae; Dioxygenases; Nitrobenzenes

PubMed: 35343758
DOI: 10.1128/aem.02437-21