Indian Journal of Microbiology最新文献

Global warming is the current threat to mankind and methane is the second most important greenhouse gas. Methanotrophs represent a group of bacteria that oxidize methane and are, therefore, environmentally very important. The cultivation of methanotrophs poses a challenge due to their specific cultivation conditions. Rice fields are important habitats where methanotrophs play a vital role in methane mitigation. We recently cultured Methylomicrobium strain RS1 from a rice field in India and briefly suggested it to be a member of putative novel species (Ca. Methylomicrobium oryzae) using draft genome-based ANI and DDH parameters (Rahalkar et al. in Front Microbiol 12:1–15, 2021). This culture presented challenges in terms of weak growth and inability to get cryopreserved. In the present work, we carried out the polyphasic characterization of this novel species which encompasses its chemotaxonomic, metabolic properties and salient genome features. Ca. Methylomicrobium oryzae is the first cultured methanotroph to be described from rice field habitats and could be an essential player in these ecosystems. It awaits further studies. Methylomicrobium sequences have been reported from rice fields but there were no reports of cultivation of members from this group, and this is the first report. Due to its growth challenges and fastidious nature of growth, inability to be cryo-preserved, and additionally due to legislations imposed on countries including India, the culture cannot be deposited in two international culture collections in other foreign countries. Within India, Ca. Methylomicrobium oryzae RS1 is maintained in our laboratory as a live culture at 4 °C and at room temperature (25–30 °C) by subculturing after intervals. Our laboratory is part of the WDCM approved culture collection MCM, and the culture is registered as MCMB-1473. It is also deposited in another internationally recognized culture collection: NCMR, Pune with the accession number MCC-4197. The draft genome of Ca. Methylomicrobium oryzae RS1 is available as JAERVK01.1.

The rapid emergence of carbapenem-resistant Enterobacteriaceae is a critical public health issue across the globe. Widespread antibiotic resistance to multiple drugs has been reported in clinical isolates of Enterobacter hormaechei. In the present investigation, we report the whole genome sequencing (WGS) of a multi-drug resistant (MDR), clinical strain of E. hormaechei, GC26 isolated from Thiruvananthapuram, Kerala (India). Using the Oxford Nanopore sequencing platform, we identified key drug-resistance genes (bla, tet, armA, qnrB, and fos) and virulence genes (fimD, csgD, csgE, csgF, and csgG) in GC26. Multi-Locus Sequence Typing (MLST) analysis of GC26 revealed a novel sequence type (ST*ba28). Phylogenetic analysis showed that the GC26 genome occupies a distinct branch within the Enterobacter genus, closely related to Indian strains of E. hormaechei rather than the global population. This study provides valuable insights into the genetic basis of multidrug resistance in E. hormaechei. These findings underscore the critical need for continuous monitoring and robust epidemiological surveillance of MDR E. hormaechei strains.

Phytohormones has produced by endophytic bacteria promote the development and yield in plants. To investigate the role of endophytic bacteria on the soil properties and the growth of ginger, a net house experiment was carried. The experiment was used four treatments (Control, Bacillus subtilis IGPEB 34, Bacillus pumilis IGPEB 37, and Bacillus altitudinis IGPEB 20). Bacillus subtilis IGPEB 34 and B. pumilis IGPEB 37 significantly increased plant growth (the plant height, leaf number, leaf length, and leaf width) as compared to the control treatment. Moreover, inoculation of B. subtilis IGPEB 34 treatment significantly enhanced the total chlorophyll, chlorophyll a, chlorophyll b and carotenoid contents. In comparison to the control, inoculation B. subtilis IGPEB 34 treatment significantly enhanced the catalase, invertase and phosphatase activities in soil, the total phosphorus (P), potassium (K), carbon (C), and humus contents in the soil. The results concluded that B. subtilis IGPEB 34 strain positively influence the soil nutrients, along with morphological and physiological characteristics of ginger.

Viral infections are the most common etiological agents behind a wide range of human illnesses, with significant and widespread effects on human health. Vaccines have been developed to combat viral infectious diseases in various ways. However, the high rate of mutation in viruses, specifically RNA viruses, makes vaccines and medications for viral infectious diseases ineffective. Meanwhile, published research continues to offer insight into the efficacy of probiotics as antiviral agents. Various clinical findings reveal those specific probiotic strains aid in the prevention of viral and bacterial infections. Probiotics have been used to prevent and treat common viral infections such as rotavirus, coronavirus, hepatitis, human papillomavirus, human immunodeficiency virus, and herpes simplex viruses etc. The studies compiled in this review demonstrate the value of probiotics in the treatment and prevention of several viral infections using in vitro and in vivo trials in both experimental animals and humans and also provide perspectives on probiotics' probable antiviral mechanisms. Although the initial findings are promising, the current research is limited by small sample sizes, short study durations, and a lack of diversity in population groups. Consequently, further research with larger, more diverse cohorts and extended follow-up periods is necessary to thoroughly assess and confirm the effectiveness of this probiotic treatment against these severe infectious diseases.

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Endophytes associated with medicinal plants hold substantial promise as a novel source for therapeutics development. In this study, 11 endophytic fungi and 9 endophytic bacteria were isolated from the roots of Pueraria thomsonii. In the preliminary screening, the ethyl acetate extract of the Apiospora marii FG-Z21 displayed strong inhibitory effects against drug-resistant bacteria Enterococcus faecalis and Methicillin-resistant Staphylococcus aureus (MRSA) with MIC values of 1.563 and 0.098 mg/mL, respectively. Furthermore, this extract exhibited significant inhibitory effects on A549 cells with a GI₅₀ value of 0.036 mg/mL and demonstrated a good antioxidant property with an EC₅₀ value of 1.869 mg/mL. Further investigation of the active ethyl acetate extract of A. marii FG-21 led to the isolation of 4-hydroxybenzoic acid (1), 2-acetamidobenzoic acid (2), benzoic acid (3), dibutyl phthalate (4), 3,4-dimethoxybenzoic acid (5), schizostatin (6), ethyl pyroglutamate (7), and anthranilic acid (8). Notably, compounds 3, 1 and 2 exhibited significant cytotoxicity against A549 cells with GI₅₀ values ranging from 4.97 to 83.08 µg/mL. On the other hand, compounds 4, 5 and 6 demonstrated potent inhibition of E. faecalis growth with low MIC values ranging from 2 to 4 µg/mL. Our study provides a comprehensive exploration of P. thomsonii-derived endophytes and their compounds highlighting their significant bacteriostatic, antioxidative, and cytotoxic activities that may potentially contribute to drug discovery paradigms.

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In this work, we used a biocompatible and safe approach for the treatment of health-threatening diseases using the Spinacia oleracea plant. Practically, Ag nanoparticles were green synthesized applying Spinacia oleracea to use against breast cancer cells (MCF-7 and MDA-MB-231 cell lines) and bacteria (S. aureus, S. epidermidis, and P. aeruginosa). Next, analytical techniques (FT-IR, XRD, DLS, TEM, and SEM) were employed for the characterization of nanoparticles. Nanometric size (10 nm to 25 nm in diameter), crystallinity, and spherical and semi-spherical morphology were determined for the biosynthesized Ag nanoparticles. Then, several biomedical tests (MIC, MBC, cell viability (MTT), quantitative gene expression (qRT-PCR), cell cycle arrest, and apoptosis) were performed for investigating the cell suppression capability of Ag nanoparticles and extracted plant precursor. These results indicated MIC of 20 nM, 35 nM, and 35 nM for S. epidermidis, P. aeruginosa, and S. aureus after treatment with Ag nanoparticles, respectively. Cell viabilities of 35% to 90% (for plant precursor) and 55% to 85% (for Ag nanoparticles) were observed for both cancer cells. Expression levels of BRCA1 (3 to 6 folds decrease), BRCA2 (4 to 15 folds decrease), Caspase9 (3.5 folds increase), Bcl2 (3 folds decease), Beclin1 (no considerable shift), and ATG (1.3 folds increase) genes were ascertained in cancer cells after treatment with Ag nanoparticles. Also, the cell cycle arrest (18- and 19-fold increase for MCF-7 and MDA-MB-231, respectively) and apoptosis (22% necrosis for MCF-7 and 17.5% apoptosis for MDA-MB-231) assays have remarkably confirmed the potency of biosynthesized Ag nanoparticles in the treatment of diseases.

Candida tropicalis is an opportunistic yeast pathogen that has the ability to develop resistance to fluconazole. This study evaluated the effect of fluconazole on the rise of phenotypic switching in C. tropicalis, an event that affects virulence in this species. C. tropicalis clinical isolate 49.07 switched reversibly at high frequency (10⁻¹ to 10⁻²) after growth in presence of subinhibitory concentration of fluconazole (0.0625 µg/mL). Phenotypic switching resulted in colonies exhibiting Star and Micro morphologies. A decrease in sensitivity to fluconazole for the Star morphotype was observed. Colonies of both switched morphotypes were associated with higher percentages of filamentous growth relative to the Smooth morphotype (clinical isolate pattern). Under filament-inducing conditions, filamentation was increased for the Star morphotype. The Star and Micro phenotypes exhibited reduced biofilm compared to the Smooth morphotype. The expression of transcription factors (EFG1 and WOR1) was increased in the Micro morphotype compared to the Smooth colonies. Our findings indicate that in vitro exposure of C. tropicalis to fluconazole may promote phenotypic switching and the occurrence of switched morphotypes with altered virulence traits.

Antibiotic manufacturing sites act as the hotspot for the dissemination of antibiotic resistance. The present study explores the resistome and secondary metabolites profile associated with the sludge of two pharmaceutical industries located in Delhi and Mysore, India. It confirmed that the pharma sludge contains complex microbiome and resistome. The presence of antibiotic-resistant genes (ARGs), class I integrons, and secondary metabolite genes (NRPs and PKs) was confirmed using PCR. Metagenomic tools like ResFinder 3.2, DeepARG, BusyBee, MG-RAST, and CoMET universe were used to analyze pharmaceutical sludge metagenome. Proteobacteria was found abundant in both metagenomes, followed by firmicutes & bacteriodetes. KEGG analysis predicted the expression of vancomycin, Pandrug, antifolate resistance pathway in both metagenomes. Resfinder predicted the presence of aminoglycoside, macrolide, and sulphonamide resistance genes in both metagenomes. DeepARG analysis classified ARGs in 28 (Arbro) & 27 (Mysore) ARG category and 431 & 368 ARG class. Further, CoMET universe indicated the presence of biosynthetic gene clusters like type II polyketide biosynthesis, Nonribosomal polypeptide biosynthesis, vancomycin & tetracycline, and macrolide biosynthesis. The present study provides primary insight about the diversity of secondary metabolites clusters present in pharmaceutical sludge. Microbes residing in such environment grows under higher selection pressure and produce various secondary metabolites. These metabolites could be exploited for the discovery of novel metabolites with antimicrobial potential and combating AMR. In future, the author aims to clone metagenome in expression vector (BAC/YAC vectors) for the discovery of novel secondary metabolites.

Paratuberculosis, caused by Mycobacterium avium subsp. paratuberculosis (MAP), is an incurable chronic disease affecting virtually all ruminants. Although buffaloes are usually considered to be more resistant than cattle, bubaline paratuberculosis displays similar gross and histological lesions. The association of MAP with human Crohn’s disease poses a high risk of infection for slaughterhouse and dairy farm workers. The objective of the present study was to identify subclinical paratuberculosis in buffaloes slaughtered at Mhow cantonment abattoir, Madhya Pradesh, India. A total of 150 paired samples comprising serum (N = 50), tissues of the intestine (N = 50), and mesenteric lymph nodes (N = 50) from each animal were collected randomly from 50 buffaloes over a period of 3 months to perform the diagnosis by competitive ELISA for anti-MAP IgG detection in serum samples. Tissue samples were subjected to histopathology to classify the lesions in hematoxylin–eosin-stained tissue sections and to detect acid-fast bacilli in sister tissue sections on Ziehl–Neelsen staining. Anti-MAP antibodies were detected in 22.0% (11/50) of the serum samples. Among tissue samples, grade I, II, III, and IV lesions were observed in 24, 22, 4, 0 ileum, and 20, 24, 5, and 1 mesenteric lymph node samples, respectively. Acid-fast bacilli were observed in 6 ileum and 11 mesenteric lymph node samples. Overall, histological findings were more defined and illustrative than ELISA and can be used for the identification of paratuberculosis among slaughtered animals, especially in laboratories with limited resources. The findings also suggest an urgent requirement for the adoption of paratuberculosis control measures in the area.

Human Immunodeficiency Virus (HIV) is a major global healthcare burden. Current lifelong antiretroviral therapy drastically improves life expectancy but do not cure HIV. Therefore, at the existing growth rates, it is estimated that around 42 million people will be living with HIV by 2030 worldwide. A cure for HIV is need of the hour which could come in the form of remission (durable viral control without ART) or eradication (complete removal of latent replication-competent virus). In this review, we discuss recent advances in basic, applied and clinical aspects of latent HIV reservoirs including its tissue locations, cell types, cell properties, genomic integration sites and its significance, mechanism of reservoir seeding and methods to study the reservoirs. Natural models of functional cure which include elite controllers, viremic controllers, long term non-progressors and post-treatment controllers are discussed. Recent advances towards a functional HIV cure are discussed under headings; CCR5Δ32/Δ32 stem cells transplantation, shock and kill strategy, block and lock strategy, gene therapy and combined strategies.