Unclassified Mycobacterium Research Articles

Shotgun metagenomic analysis reveals the diversity of PHA producer bacterial community and PHA synthase gene in Addis Ababa municipal solid waste disposal area ‘Qoshe’

BackgroundPolyhydroxyalkanoates (PHAs) are naturally produced biopolymers with significant scientific and biotechnological potential. This study aimed to investigate the diversity of the PHA-producing bacterial community and PhaC genes in soil samples collected from a municipal solid waste disposal site known as “Qoshe” in Addis Ababa, Ethiopia, using a shotgun metagenomics approach. The SqueezeMeta pipeline was used to analyze the microbial community in the waste samples. A CD search against the TIGRFAM protein family database was performed to identify the complete-length multidomain sequences of PhaC genes and classify them into their respective classes. Statistical analysis and data visualization were performed using RStudio with R version 4.2.3.ResultsThe findings of this study suggest that known and unknown taxa likely contribute to the phaC genes of municipal solid waste. Taxonomic profiling of the metagenomic data revealed that the majority of the PHA-producing taxa belonged to the phylum Proteobacteria (80%), followed by Actinomycetota (16.5%). Furthermore, this study identified Thiomonas and unclassified Mycobacterium as the main contributors to class I PhaC genes. Class II PhaC genes are predominantly associated with the Pseudomonadaceae family, followed by unclassified Hyphomicrobials and Acidimicrobiales. Class III PhaC genes are abundantly related to the Methylococcaceae family, specifically the Methylocaldum genus. The analysis of PhaC gene sequences revealed high level of diversity, with a significant proportion of putative PhaC genes exhibiting low sequence identity with each other and PhaC gene in the database. Notably, the sequence variation observed within the same PhaC gene classes suggests the potential presence of previously unidentified PhaC gene variants.ConclusionsOverall, this research improves our understanding of the diversity of PHA-producing taxa and PhaC genes in municipal solid waste environments, providing opportunities for sustainable PHA production and waste management strategies. However, additional studies, including the isolation and characterization of specific strains, are necessary to confirm the PHA production capabilities of these strains and explore their biotechnological potential.

Harnessing next-generation sequencing to monitor unculturable pathogenic bacteria in the indoor hospital building

The hospital indoor air microbiome, a diverse range of microorganisms, gains prominence amid the COVID-19 pandemic. Elevated awareness underscores implications for patient and staff well-being. Concerns about risks to indoor air quality persist due to prolonged indoor exposure, necessitating further research on specific threats within the hospital environment. In this study, an independent culture-based approach was used to analyze the baseline core microbiome present in hospital environments, utilizing amplicon sequencing on the next-generation sequencing technology to target the V3 region of the 16S rRNA gene. Firmicutes, Proteobacteria, and Actinobacteria were the main bacterial phyla that were most isolated from the wards and clinics with different orders of abundance; Firmicutes being associated more in clinics and Actinobacteriota in wards. The bacteria Niallia taxi, Methyloversatilis universalis, unclassified Rummeliibacillus, unclassified Clostridium, and unclassified Sphingomonadaceae dominated the clinic area while ward areas reported Pseudonocardia bannensis, Rubrobacter aplysinae, unclassified Brachybacterium, unclassified Bradyrhizobium, and unclassified Mycobacterium to be the top five features. While the alpha-diversity index showed no significant differences, the beta-diversity analysis showed a significant difference between clinic and ward areas (p<0.05). Certain bacterial species associated with opportunistic pathogens as well as normal skin flora such as Methylobacterium spp., Cutibacterium spp., unclassified Sphingomonadaceae, and Anoxybacillus B spp., were also identified across all samples. The methods described in this research aim to establish a rapid and sensitive screening process that could be valuable for disease surveillance within the healthcare setting, shedding light on the potential impacts of the hospital microbiome on human illness.

Novel and rare species of nontuberculous mycobacteria by Hsp-65 gene sequencing.

Nontuberculosis mycobacterium (NTM) is the emerging group of organisms being recognized as etiological agents for diverse clinical conditions such as lymphadenitis, cutaneous, and pulmonary or disseminated lesions. Diverse background patients can acquire these infections such as immunocompetent, immunocompromised patients, or postoperative settings. Rapid addition of newer strains to this group necessitates heightened suspicion in the clinical settings. Specific requirements for cultures, biochemical testing, and molecular methods are needed to diagnose these organisms. The prospective study conducted at Nizam's Institute of Medical Sciences from January 2019 to December 2021 using various clinical samples using molecular techniques such as line probe assay and hsp-65 gene sequencing to discover new NTM species. The management is challenging since it requires prolonged treatment, multiple drugs, drug resistance, and individualization of treatment in the combination of surgery if needed. In this article, we describe three different NTM species which were not reported in India and highlight to consider these organisms in adequate clinical situation. Mycobacterium iranicum is a rare strain with quick growth and scotochromogenic colonies that are orange-colored. Eight distinct strains were discovered in clinical samples from six different countries: Two each from Iran, Italy, Greece, the Netherlands, Sweden, and the United States. Two of the strains were recovered from cerebrospinal fluid, which is unusual. Mycobacterium species AW6 is an unidentified and unclassified Mycobacterium according to NCBI taxonomy. Mycobacteria malmoense has been linked to lymphadenitis, notably cervical adenitis in children, and pulmonary infection in the majority of cases. Using Line Probe Assay and hsp-65 gene sequencing, novel and uncommon species of NTM were detected from a clinical samples, including sputum and tissue. We report three unusual species of NTMs: M. iranicum, M. species-AW6, and M. malmoense for the first time in India. Novel and rare emerging species of NTMs need to be considered in diverse clinical situations for appropriate therapy and good clinical outcomes.

Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China).

In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.

Determination of genome size and DNA homology between an unclassified Mycobacterium species isolated from patients with Crohn's disease and other mycobacteria.

The genome size of an unclassified Mycobacterium species, isolated from a patient with Crohn's disease, was determined by measurement of DNA renaturation kinetics as 3.1 X 10(9) Da. The percentage of DNA homology of this organism to DNA of related mycobacteria was evaluated by measurement of DNA renaturation with heterologous DNA. These studies supported the classification of this organism as Mycobacterium paratuberculosis but failed to distinguish between M. paratuberculosis and organisms of the Mycobacterium avium-intracellulare groups.

Spheroplastic phase of mycobacteria isolated from patients with Crohn's disease.

Two strains of an unclassified Mycobacterium species were isolated after 18 and 30 months of incubation of media inoculated with resected intestinal tissues from patients with Crohn's disease. These strains represented the third and fourth isolates of this organism from Crohn's disease patients. Ultrastructural examination of this strain and two previously isolated strains revealed the presence of spheroplasts which eventually transformed into the bacillary form of a previously unrecognized Mycobacterium species. These cell wall-deficient forms did not stain with conventional dyes and failed to grow on hypertonic media. Restriction polymorphism of the ribosomal DNA genes was used to determine the relationship between the cell wall-deficient and bacillary forms. Identical restriction patterns of the ribosomal DNA genes were found between the spheroplasts and Mycobacterium sp. isolates with EcoRI, BamHI, and XhoI restriction endonucleases, thus providing definitive evidence of their origin. Unidentified spheroplasts were isolated from an additional 12 patients with Crohn's disease, of which 7 of 10 seroagglutinated with antiserum prepared against the Mycobacterium sp. Spheroplasts were isolated from 16 of 26 (61%) patients with Crohn's disease but not from tissues of 13 patients with ulcerative colitis or 13 patients with other diseases of the bowel. These findings support the role of mycobacteria as etiologic agents in some cases of Crohn's disease.

In vitro antimicrobial susceptibility of a Mycobacterium sp. isolated from patients with Crohn's disease.

The in vitro susceptibility of three strains of an unclassified Mycobacterium sp., isolated from three patients with Crohn's disease, to 23 antimicrobial agents was determined by a modified broth dilution method with 7H9 broth containing oleic acid-albumin-dextrose-catalase, Tween 80, and mycobactin J. All three strains were susceptible to streptomycin, viomycin, rifampin, clofazimine, cefazolin, amikacin, and kanamycin and resistant to p-aminosalicylic acid, cycloserine, 2-thiophenecarboxylic acid hydrazide, trimethoprim, diaminodiphenylsulfone, sulfamethoxazole, sulfadimethoxine, polymyxin B, metronidazole, neomycin, and carbenicillin. Variable results between strains were encountered with ethambutol, ethionamide, capreomycin, amoxicillin, and cephalothin.

Characteristics of an unclassified Mycobacterium species isolated from patients with Crohn's disease.

The characteristics of an unclassified Mycobacterium sp. isolated from three patients with Crohn's disease are presented. The organism is extremely fastidious and mycobactin dependent and may require up to 18 months of incubation for primary isolation. Colony morphology is rough. Characteristics are unlike those of any presently defined species. The isolates produced postive niacin, catalase, and 2-week arylsulfatase reactions and were susceptible to neotetrazolium chloride (1:40,000), streptomycin (2 micrograms/ml), and rifampin (0.25 micrograms/ml). Chromogenicity, nitrate reduction, quantitative catalase, Tween hydrolysis, urease, tellurite reduction, pyrazinamidase, and 3-day arylsulfatase tests were negative, and the isolates were resistant to thiophene-2-carboxylic acid hydrazide (10 micrograms/ml) and isoniazid (10 micrograms/ml). Optimum growth in broth was determined to be in 7H9 medium with Dubos oleic albumin complex, Tween 80, and mycobactin J at 37 degrees C without CO2 or agitation and in low medium depth. This Mycobacterium sp. may be a subspecies or biovariant of Mycobacterium paratuberculosis, or it may represent a new species of Mycobacterium. It is suggested that this Mycobacterium sp. may play an etiological role in some cases of Crohn's disease.

Sur les acides mycoliques de P6

An α-mycolic acid was isolated from P6, an unclassified mycobacterium, scotochromogen, and its structure was determined. This acid has a chain of 80 carbons and two rings of cyclopropane. It was found that the entire structure of this α-mycolic acid was similar to that from M. smegmatis and M. phlei.

The mannophosphoinositides of the unclassified Mycobacterium P 6 .

The mannophosphoinositides of the unclassified Mycobacterium P6 (Runyon Group II) were examined by chromatographic procedures and by the incorporation of carbon-14 from guanosinediphosphate-14C-mannose into them. Contrary to another report, monomannophosphoinositide was almost certainly absent, and the usual preponderance of dimannophosphoinositides was evident.

Wax D fraction of an unclassified Mycobacterium strain.

Wax D prepared from the P-6 strain of the scotochromogenic species of Mycobacterium scrofulaceum constituted 0.3% of the dry bacilli. In the acid hydrolysates, alanine, glutamic acid, glycine, and mesodiaminopimelic acid were found as amino acid constituents. Mannose, galactose, and glucosamine were detected by paper chromatography. However, arabinose could not be detected. The quantity of hexosamine was 0.2 to 0.3%. Wax D of P-6 was found to be adjuvant-active, as revealed by a positive corneal reaction. The antigenicity of wax D of P-6 was shown by the agglutination reaction between the suspension of wax D and the anti-wax D antiserum. Periodate oxidation of the hydrosoluble portion reduced the inhibitory effect of the hydrosoluble portion on agglutination of the suspension of wax D. The light fraction of wax D had a peptide portion consisting of alanine, glutamic acid, glycine, and diaminopimelic acid and was found to be adjuvant-active in an amount of 1,000 mug.

ATYPICAL PULMONARY TUBERCULOSIS CAUSED BY UNCLASSIFIED MYCOBACTERIA.

Article1 March 1964Atypical Pulmonary Tuberculosis Caused by Unclassified MycobacteriaSAMUEL PHILLIPS, M.D., F.A.C.P., JOHN C. LARKIN JR., M.D., F.A.C.P.SAMUEL PHILLIPS, M.D., F.A.C.P.Search for more papers by this author, JOHN C. LARKIN JR., M.D., F.A.C.P.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-60-3-401 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptPatients with chronic pulmonary disease from whose sputa unclassified Mycobacteria are recovered are a problem to clinicians and public health officials. These cases are classified as "infection of lung, due to unclassified Mycobacterium" (1) but are also referred to as "atypical tuberculosis" (2). A review of 32 patients with atypical pulmonary tuberculosis treated at our hospital since 1959 is presented to illustrate various aspects of the problem.There is a marked similarity of atypical pulmonary tuberculosis to pulmonary tuberculosis in physical findings, roentgenographic appearance, positive tuberculin (Mantoux) reaction, and the presence of acid-fast bacilli in the sputum (3). On histological...

An unclassified "unclassified" Mycobacterium.

An unusual unclassified mycobacterium has been repeatedly recovered over a period of years from a 46-year-old white woman with persistent respiratory symptoms and a slowly progressive pulmonary disease. Although the mycobacterium in this case was probably an opportunistic secondary invader, it appears to have played a role in the more recent progression of symptoms and roentgenographic pulmonary changes. The organism has been thoroughly studied but fails to conform fully to any of the usual subgroups of the unclassified mycobacteria as characterized in the currently employed schema. This case report emphasizes the increasing clinical and bacteriologic importance of the unclassified mycobacteria and presents a systematic approach to their identification through careful cultural, morphologic, and biochemical characterization.