PLSDB: advancing a comprehensive database of bacterial plasmids.

Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.

Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation.

Saccharibacteria (TM7) are obligate epibionts living on the surface of their host bacteria and are strongly correlated with dysbiotic microbiomes during periodontitis and other inflammatory diseases, suggesting they are putative pathogens. However, due to the recalcitrance of TM7 cultivation, causal research to investigate their role in inflammatory diseases is lacking. Here, we isolated multiple TM7 species on their host bacteria from periodontitis patients. These TM7 species reduce inflammation and consequential bone loss by modulating host bacterial pathogenicity in a mouse ligature-induced periodontitis model. Two host bacterial functions involved in collagen binding and utilization of eukaryotic sialic acid are required for inducing bone loss and are altered by TM7 association. This TM7-mediated downregulation of host bacterial pathogenicity is shown for multiple TM7/host bacteria pairs, suggesting that, in contrast to their suspected pathogenic role, TM7 could protect mammalian hosts from inflammatory damage induced by their host bacteria.

Effects of fertilizer practice on fungal and actinobacterial cellulolytic community with different humified particle-size fractions in double-cropping field.

Cellulose plays an important role in maintaining or improving soil carbon (C) cycling and soil fertility of paddy field. There had close relationship between functional cellulose genes (cbhI and GH48) with characterize of soil organic matter chemical components (fulvic acid and humic acid) and soil physical fractions. However, there is still limited information about how functional cellulose degradation response to long-term fertilizer management and their relative importance for C sequestration under the double-cropping rice paddy field in southern of China. Therefore, the objective of this study were investigated the effects of 34-years long-term fertilizer regime on community abundance of cbhI and GH48 genes in five soil particle-size fractions (> 2000 µm, 2000-200 µm, 200-50 µm, 50-2 µm and 2-0.1 µm) by using polarization magic angle spinning 13C nuclear magnetic resonance spectroscopy. The field experiment was included four different fertilizer treatments: chemical fertilizer alone (MF), rice straw and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that distribution of soil humus and cellulolytic microbial community abundance was significant increased under long-term application of crop residue and organic manure condition. And the FA, HA and HM C contents in > 2000 µm and 2000-50 µm fractions with MF, RF and OM treatments were significant higher than that of CK treatment. Meanwhile, the alkyl C and Oalkyl C groups of FA and HA in > 2000 µm fraction with MF, RF, OM and CK treatments were higher than that of the other fractions. There had higher AL% and lower ARO% of FA and HA in different particle-size fractions with MF, RF, OM and CK treatments. The results indicated that abundance of cbhI and GH48 genes in different particle-size fractions with RF and OM treatments were significant increased, compared with CK treatment. There had significant positive correlation between soil humus C components (FA and HA) with abundance of cbhI and GH48 genes, and the o-alkyl C and AL% of FA were positively correlated with abundance of cbhI and GH48 genes. As a result, the community abundance of cbhI and GH48 genes were significant increased under combined application of crop residue and organic manure with chemical fertilizer condition.

Eggerthella lenta bacteremia successfully treated with ceftizoxime: case report and review of the literature.

Eggerthella lenta is a normal human microflora that is anaerobic, non-sporulating, and Gram positive. However, an increasing number of studies have shown that it could also be an important pathogen for humans, even causing life-threatening infection under certain conditions. However, understanding its pathogenic mechanism and treatment options still need to be improved; more clinical data are needed to explore it further. In this article, we report a case of ceftizoxime-cured E. lenta bacteremia and review the recent literature to provide more clinical data for the diagnosis of E. lenta bacteremia. Our report suggests that the frequency of E. lenta bacteremia is increased in patients with hematologic or solid organ cancer, diabetes mellitus and also in those with appendicitis.

Actinomycetes isolates of arid zone of Indian Thar Desert and efficacy of their bioactive compounds against human pathogenic bacteria.

Twenty-six morphotypes of actinomycetes bacteria were isolated from the soils of arid zone of Indian Thar desert, Rajasthan. A significant and positive correlation was found between density of actinomycetes isolates and availability of nitrogen in sandy soil of arid zone suggesting the influence of soil nitrogen on occurrence and propagation of actinomycetes in this region. Molecular identification based on 16S rRNA gene sequencing revealed that the bacterial isolates belong to four actinomycetes genera, viz. Streptomyces (22 species), Nocardiopsis (two species), Saccharomonospora (one species) and Actinoalloteichus (one species). The preliminary screening of 26 isolates against five human pathogenic bacteria, viz. Escherichia coli, Vibrio cholera, Salmonella enterica typhimurium, Staphylococcus aureus and Enterococcus faecalis, showed that only four isolates, viz. Streptomyces sp. (ITD-27), S. enissocaesilis (ITD-29), S. Malachitospinus (ITD-35) and Streptomyces sp. (ITD-47), had antibacterial activity. The secondary screening of these four isolates revealed that the isolate S. malachitospinus (ITD-35) showed the maximum growth inhibition zone and inhibited the growth of all tested gram-positive and gram-negative pathogenic bacteria. Gas chromatography-mass spectrometry analysis of S. malachitospinus (ITD-35) cultural filtrate in n-butanol solvent identified three antibacterial compounds of medicinal significance, viz. 3-octanone, neopentyl isothiocyanate and 2-methyl butyl isothiocyanate.

Detection of co-infection of Gardnerella vaginalis and Atopobium vaginae using qualitative PCR: A better predictor of bacterial vaginosis.

The present study aimed to determine the utility of detection of co-infection of Gardnerella vaginalis and Atopobium vaginae using qualitative PCR for diagnosing bacterial vaginosis (BV). Vaginal samples (n = 385) categorized as positive (n = 108) or negative (n = 208) for bacterial vaginosis based on the Nugent scoring system, were analyzed for the presence of G. vaginalis and A. vaginae by conventional PCR. We compared the sensitivity, specificity, positive predictive value, negative predictive value and odds ratio for the detection of each bacterium alone with the combination of the two bacteria for diagnosing BV. The detection of co-infection of the two bacteria demonstrated a sensitivity of 96%, a specificity of 82.9%, a positive predictive value of 68.5%, a negative predictive value of 98.2% with an odds ratio of 116 (CI -32 - 409). In our study, we found a high sensitivity, specificity, negative predictive value and odds ratio for the detection of co-infection of A. vaginae and G. vaginalis for the diagnosis of BV.

Whole genome sequencing and genome annotation of Dermacoccus abyssi strain HZAU 226 isolated from spoiled eggs.

Dermacoccus abyssi strain HZAU 226 is a spoilage bacterium isolated from eggs. So far, there are still few genomic resources available on the Dermacoccus abyssi. Here, we reported the complete genome sequence of Dermacoccus abyssi strain HZAU 226. High-quality DNA was extracted using the Qiagen kit, then single-molecule sequencing was performed by GridION sequencer. The raw data was quality-controlled and assembled to obtain the final genome, which consisted of a complete genome of 2,992,060 bp circular chromosome and a 64,524 bp plasmid. The structural and functional annotations of the genome were achieved through the analysis of different available databases, including antibiotic resistance genes, secondary metabolite synthesis genes and stress-related genes. Meanwhile, comparative genomic analyses of the strains were also performed. This is the first report on the complete genome of Dermacoccus abyssi, which will provide genomic resources for the study of spoilage bacteria in eggs.

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis.

Plant microbiota colonize all organs of a plant and play crucial roles including supplying nutrients to plants, stimulating seed germination, promoting plant growth, and defending plants against biotic and abiotic stress. Because of the economic importance, interactions between citrus and microbes have been studied relatively extensively, especially citrus-pathogen interactions. However, the spatial distribution of microbial taxa in citrus trees remains under-studied. In this study, Citrus reticulata cv. Chachiensis was examined for the spatial distribution of microbes by sequencing 16S rRNA genes. More than 2.5 million sequences were obtained from 60 samples collected from soil, roots, leaves, and phloem. The dominant microbial phyla from all samples were Proteobacteria, Actinobacteria and Acidobacteria. The composition and structure of microbial communities in different samples were analyzed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial species between samples were analyzed and the indicator microbes of each sample group were identified. Our results suggested that the microbial communities from different tissues varied significantly and the microenvironments of tree tissues could affect the composition of its microbial community.

Bacterial wilt of dry beans caused by Curtobacterium flaccumfaciens pv. flaccumfaciens: A new threat from an old enemy.

Bacterial wilt and tan spot of dry beans (family Fabaceae), caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is an important emerging disease threatening the edible legume industry around the globe. The management of bacterial wilt has been a major problem since its original description in 1922. This is in part due to the seedborne nature of the pathogen allowing the bacterium to be transmitted long distances via infected seeds, as well as a lack of detailed molecular information concerning the pathogenicity repertoires and virulence determinates of the pathogen. Identification can also be difficult owing to the presence of five different colony colour variants (i.e., yellow, orange, pink, purple, and red) on culture media. In this review, we provide an overview of the aetiology, epidemiology, and management strategies of bacterial wilt disease. First, a comprehensive and comparative symptomology of the disease on different dry bean species is described. Then, the taxonomic history of the causal agent and utility of high-throughput sequencing-based approaches in the precise characterization of the pathogen is explained. Furthermore, we provide an updated outline on the global distribution of the pathogen, highlighting expansion of the causal agent into the areas with no history of the disease until the beginning of the current century. Finally, because there are limited options for use of conventional pesticides against the pathogen, we highlight the use of integrated pest management strategies, for example quarantine inspections, resistant cultivars, and crop sanitation, to combat the risk of bacterial wilt disease in the dry bean industry. DISEASE SYMPTOMS: Interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. Seed discolouration to yellow, orange, pink, or purple is seen in white-seeded cultivars. HOST RANGE: Causes bacterial wilt and tan spot disease on edible dry beans in the Fabaceae family, including common bean (Phaseolus vulgaris), cowpea (Vigna unguiculata), mungbean (Vigna radiata), soybean (Glycine max), as well as a number of weed species. TAXONOMIC STATUS OF THE PATHOGEN: Bacteria; phylum Actinobacteria; order Actinomycetales; suborder: Micrococcineae; family Microbacteriaceae; genus Curtobacterium; species Curtobacterium flaccumfaciens. SYNONYMS: Corynebacterium flaccumfaciens subsp. flaccumfaciens; Corynebacterium flaccumfaciens pv. flaccumfaciens, Corynebacterium flaccumfaciens, Phytomonas flaccumfaciens, Bacterium flaccumfaciens. MICROBIOLOGICAL PROPERTIES: Multicoloured (yellow, orange, pink, purple, and red), gram-positive, aerobic, curved rod, nonspore-forming, polar flagellated, motile cells. DISTRIBUTION: Widespread in America (Brazil, Canada, and the USA), Australia, and Iran. Restricted occurrence in Africa and Europe. PHYTOSANITARY CATEGORIZATION: EPPO A2 list no. 48, EU Annex II/B.

Characterization of genes responsive to osmotic and oxidative stresses of the sugarcane bacterial pathogen Leifsonia xyli subsp. xyli.

Leifsonia xyli subsp. xyli (Lxx) colonizes the xylem vessels of sugarcane, a plant niche where microorganisms are highly exposed to oxidative and osmotic stresses. This study performed an in silico analysis of the genome of Lxx and characterized 16 genes related to the detoxification of oxidative species (peroxidases, O2- dismutases, and methionine reductases) and to the production and transport of osmolytes and analyzed their expression in vitro after 30, 60, and 120 min of exposure to H2O2 or PEG. The PAGE activity of superoxide dismutase (Mn-SOD as confirmed by inhibition tests) and of catalase (CAT) and the accumulation of trehalose were also assessed. Exposure to H2O2 increased the expression of most oxidative-responsive genes and decreased the expression of those related to osmotic responses, whereas the opposite occurred after exposure to PEG. The isoform profiles of CAT and Mn-SOD shifted in response to H2O2 but not to PEG and Lxx cells accumulated more trehalose over time after exposure to PEG compared with non-exposed cells. The experimental results validated the in silico analysis and indicated that this obligate endophytic parasite has multiple and functional mechanisms to combat the stresses imposed by its host.

Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab.

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

Multiple Introductions of Tomato Pathogen Clavibacter michiganensis subsp. michiganensis into Iran as Revealed by a Global-Scale Phylogeographic Analysis.

Tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is one of the most important seed-borne tomato diseases around the globe. The disease was initially reported in 1993 in Iran, and it became a rising threat for the multibillion dollar tomato industry of the country during the last decade. In this study, using phylogeographic analyses, we determined genetic diversity and geographic distribution of C. michiganensis subsp. michiganensis in Iran. Our field surveys showed that the pathogen is expanding into the southern and eastern areas of the country. Furthermore, multilocus sequence analysis and typing (MLSA/MLST) using the sequences of five housekeeping genes (atpD, gyrB, ppk, recA, and rpoB) revealed that 37 C. michiganensis subsp. michiganensis strains isolated in Iran had high genetic diversity and placed in 15 sequence types (STs), while all the available 184 worldwide C. michiganensis subsp. michiganensis sequences were placed in 43 STs. MLSA divided the worldwide C. michiganensis subsp. michiganensis strains into two phylogroups (I and II). Among the 37 strains isolated in Iran, 30 strains clustered in phylogroup I, while 7 strains clustered in phylogroup II. Phylogeographic data inferred from the allelic profile of the five housekeeping genes suggested multiple introductions of C. michiganensis subsp. michiganensis inoculum into Iran, while the geographic origin of the Iranian C. michiganensis subsp. michiganensis strains remains undetermined. Further analyses using higher numbers of strains are warranted to decipher the evolutionary history of C. michiganensis subsp. michiganensis in Iran. Additionally, stricter seed/transplant inspections are recommended to reduce the risk of pathogen expansion to areas with no history of the disease.IMPORTANCEClavibacter michiganensis subsp. michiganensis, the causal agent of tomato bacterial canker disease, is one of the economically important pathogens of solanaceous crops (e.g., eggplant, pepper, and tomato) around the world. The disease occurs in many countries, with a particular importance in regions characterized by high precipitation and humid environmental conditions. As a seed-borne pathogen, C. michiganensis subsp. michiganensis is included in the A2 (high risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Bacterial canker disease was reported for the first time in 1993 in Iran, while the geographic distribution, genetic diversity, and phylogenetic position of the causal agent remain undetermined. In this study, using the multilocus sequence analysis and typing (MLSA/MLST) approach, we provided a phylogeographic scheme for the C. michiganensis subsp. michiganensis strains isolated in Iran. Furthermore, global-scale phylogenetic analyses led to determination of phylogenetic position of Iranian C. michiganensis subsp. michiganensis strains among worldwide population of the pathogen. Based on diversity parameters and population structure, we suggest relatively higher genetic diversity of the bacterial canker pathogen in Iran than has so far been observed in the other areas of the world. Results obtained in this study provide a novel insight into the genetic diversity and population structure of the bacterial canker pathogen on a global scale.

An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis.

Bacterial vaginosis (BV) is the most common cause of vaginal discharge. It is associated with an increased risk of preterm delivery, pelvic inflammatory disease, and an increased risk of acquisition of sexually transmitted infections including human immunodeficiency virus (HIV). The epidemiology of BV supports sexual transmission. However, its etiology remains unknown. At the center of the debate is whether BV is caused by a primary pathogen or a polymicrobial consortium of microorganisms that are sexually transmitted. We previously published a conceptual model hypothesizing that BV is initiated by sexual transmission of Gardnerella vaginalis. Critics of this model have iterated that G. vaginalis is found in virginal women and in sexually active women with a normal vaginal microbiota. In addition, colonization does not always lead to BV. However, recent advances in BV pathogenesis research have determined the existence of 13 different species within the genus Gardnerella. It may be that healthy women are colonized by nonpathogenic Gardnerella species, whereas virulent strains are involved in BV development. Based on our results from a recent prospective study, in addition to an extensive literature review, we present an updated conceptual model for the pathogenesis of BV that centers on the roles of virulent strains of G. vaginalis, as well as Prevotella bivia and Atopobium vaginae.

Interleukin-17 and matrix metalloprotease-9 expression in the mycetoma granuloma.

Mycetoma is a persistent, progressive granulomatous inflammatory disease caused either by fungi or by bacteria. Characteristic of this disease is that the causative agents organise themselves in macroscopic structures called grains. These grains are surrounded by a massive inflammatory reaction. The processes leading to this host tissue reaction and the immunophenotypic characteristics of the mycetoma granuloma are not known. Due to the massive immune reaction and the tissue remodeling involved, we hypothesised that the expression levels of interleukin-17 (IL-17) and matrix metalloprotease-9 (MMP-9) in the mycetoma granuloma formation were correlated to the severity of the disease and that this correlation was independent of the causative agent responsible for the granuloma reaction. To determine the expression of IL-17 and MMP-9 in mycetoma lesions, the present study was conducted at the Mycetoma Research Centre, Sudan. Surgical biopsies from 100 patients with confirmed mycetoma were obtained, and IL-17 and MMP-9 expression in the mycetoma granuloma were evaluated immunohistochemically. IL-17 was mainly expressed in Zones I and II, and far less in Zone III. MMP-9 was detected mainly in Zones II and III, and the least expression was in Zone I. MMP-9 was more highly expressed in Actinomadura pelletierii and Streptomyces somaliensis biopsies compared to Madurella mycetomatis biopsies. MMP-9 levels were directly proportional to the levels of IL-17 (p = 0.001). The only significant association between MMP9 and the patients' characteristics was the disease duration (p<0.001). There was an insignificant correlation between the IL-17 levels and the patients' demographic characteristics.

An update on the role of Atopobium vaginae in bacterial vaginosis: what to consider when choosing a treatment? A mini review.

INTRODUCTION: Bacterial vaginosis (BV) is the most common vaginal disorder in reproductive-age women. The condition is characterised by the replacement of a healthy, lactobacilli-dominated vaginal microbiota by anaerobic and facultative anaerobic bacteria. BV increases the risk of acquisition of STIs and is associated with pregnancy complications. Although the composition of the bacteria in BV varies between individuals, there are some species such as Gardnerella, Atopobium, Mycoplasma, Snethia, Megasphera, Dialister, etc., that are found most frequently. MATERIAL AND METHODS: Literature research to the importance of Atopobium vaginae in BV and treatment options. RESULTS: Atopobium (A.) vaginae is an important component of the complex abnormal vaginal flora in BV; even though A. vaginae, like Gardnerella vaginalis, has also been detected in the normal flora, it is much more common in BV patients. A. vaginae has been shown to play an important role in the pathophysiology of BV and is thought to be at least a partial cause of the known negative sequelae. The presence of A. vaginae in the BV-associated biofilms and its resistance to some antimicrobial substances has been described - this seems to have a major impact on treatment outcome. CONCLUSION: Current scientific data demonstrate that dequalinium chloride (Fluomycin®) is one of the valid therapeutic options for BV treatment, since it displays a broad antimicrobial spectrum against relevant vaginal pathogens, especially against G. vaginalis and A. vaginae, without having safety concerns.

Keratinocyte infection by Actinomadura madurae triggers an inflammatory response.

BACKGROUND: Actinomycetoma is a syndrome of the skin characterized by chronic inflammation and lesions with nodular grain-like structures. The most common aetiological agents are Nocardia brasiliensis and Actinomadura madurae. In response to infection with these organisms the body produces an inflammatory immune response in the skin. The aim of the present study was to determine the production of chemokines, pro-inflammatory cytokines, antimicrobial peptides and the expression of Toll-like receptors (TLRs) in keratinocytes infected by A. madurae. METHODS: A cell line of HaCaT keratinocytes was infected with A. madurae at a multiplicity of infection of 20:1 for 2 h and the samples were collected from 2 to 72 h post-infection. Intracellular replication of the bacterium was evaluated by counting of colony-forming units, the TLR expression and antimicrobial peptide production were assayed by confocal microscopy and chemokine and pro-inflammatory cytokine levels were determined by enzyme-linked immunosorbent assay. RESULTS: Early in the infection, A. madurae was able to achieve intracellular replication in keratinocytes, however, the cells eventually controlled the infection. In response to the infection, keratinocytes overexpressed TLR2 and TLR6, produced high concentrations of cytokines monocyte chemoattractant protein-1, interleukin 8, human ß-defensin-1, human ß-defensin-2 and LL37 and low levels of tumour necrosis factor α. CONCLUSIONS: The human keratinocytes contribute to the inflammatory process in response to A. madurae infection by overexpressing TLRs and producing chemokines, pro-inflammatory cytokines and antimicrobial peptides.

Selenium Nanocomposites Having Polysaccharid Matrices Stimulate Growth of Potato Plants in Vitro Infected with Ring Rot Pathogen.

The influence of nanocomposites (NC) of selenium in matrices of arabinogalactan (Se/AG) and starch (Se/St) on in vitro vegetation of potato plants, peroxidase activity, and reactive oxygen species has been thoroughly studied. It has been shown that these nanocomposites of selenium have antimicrobial effect to the phytopathogenic bacterium Clavibacter michiganensis ssp. sepedonicus (Cms). In the present investigation, it has been shown that Se/AG NC (6.4% of Se) and Se/St NC (12.0% of Se) have no negative impact on the potato plants healthy and Cms infected, while stimulating their growth, number of leaves and weight of the vegetative part. Se/AG NC has shown a positive effect on potato plants by increasing its immune status by increasing the ROS content and increasing the peroxidase activity. With the use of the element analysis technique, it has been shown that scrutinized nanocomposites are not accumulated in potato plants after the bactericidal processing with the nanocomposites. Se/AG NC and Se/St NC as potential agents used for treatment of potato plants against pathogenic bacteria.

Lung inflammation and disease: A perspective on microbial homeostasis and metabolism.

It is now well appreciated that the human microbiome plays a significant role in a number of processes in the body, significantly affecting its metabolic, inflammatory, and immune homeostasis. Recent research has revealed that almost every mucosal surface in the human body is associated with a resident commensal microbiome of its own. While the gut microbiome and its role in regulation of host metabolism along with its alteration in a disease state has been well studied, there is a lacuna in understanding the resident microbiota of other mucosal surfaces. Among these, the scientific information on the role of lung microbiota in pulmonary diseases is currently severely limited. Historically, lungs have been considered to be sterile and lung diseases have only been studied in the context of bacterial pathogenesis. Recently however, studies have revealed a resilient microbiome in the upper and lower respiratory tracts and there is increased evidence on its central role in respiratory diseases. Knowledge of lung microbiome and its metabolic fallout (local and systemic) is still in its nascent stages and attracting immense interest in recent times. In this review, we will provide a perspective on lung-associated metabolic disorders defined for lung diseases (e.g., chronic obstructive pulmonary disease, asthma, and respiratory depression due to infection) and correlate it with lung microbial perturbation. Such perturbations may be due to altered biochemical or metabolic stress as well. Finally, we will draw evidence from microbiome and classical microbiology literature to demonstrate how specific lung morbidities associate with specific metabolic characteristics of the disease, and with the role of microbiome in this context. © 2018 IUBMB Life, 71(1):152-165, 2019.

Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds.

BACKGROUND: Actinobacteria from freshwater habitats have been explored less than from other habitats in the search for compounds of pharmaceutical value. This study highlighted the abundance of actinobacteria from freshwater sediments of two rivers and one lake, and the isolates were studied for their ability to produce antimicrobial bioactive compounds. RESULTS: 16S rRNA gene sequencing led to the identification of 84 actinobacterial isolates separated into a common genus (Streptomyces) and eight rare genera (Nocardiopsis, Saccharopolyspora, Rhodococcus, Prauserella, Amycolatopsis, Promicromonospora, Kocuria and Micrococcus). All strains that showed significant inhibition potentials were found against Gram-positive, Gram-negative and yeast pathogens. Further, three biosynthetic genes, polyketide synthases type II (PKS II), nonribosomal peptide synthetases (NRPS) and aminodeoxyisochorismate synthase (phzE), were detected in 38, 71 and 29% of the strains, respectively. Six isolates based on their antimicrobial potentials were selected for the detection and quantification of standard antibiotics using ultra performance liquid chromatography (UPLC-ESI-MS/MS) and volatile organic compounds (VOCs) using gas chromatography mass spectrometry (GC/MS). Four antibiotics (fluconazole, trimethoprim, ketoconazole and rifampicin) and 35 VOCs were quantified and determined from the methanolic crude extract of six selected Streptomyces strains. CONCLUSION: Infectious diseases still remain one of the leading causes of death globally and bacterial infections caused millions of deaths annually. Culturable actinobacteria associated with freshwater lake and river sediments has the prospects for the production of bioactive secondary metabolites.