Microbiology

Microbiome: A New Lease to Microbiology

A Glimpse into the Microbiota of Marketed Ready-to-Eat Crickets ( Acheta domesticus ) Abstract The present study was aimed to get an insight into the bacterial biota of ready-to-eat small crickets (Acheta domesticus) already marketed in the European Union. 16S rRNA gene of the DNAs extracted from thirty-two samples of ready-to-eat crickets commercialized by 4 European Union producers located in Austria, Belgium, France and the Netherlands (2 batches per producer) was analyzed by Polymerase Chain Reaction–Denaturing Gradient Gel Electrophoresis (PCR–DGGE). The species belonging to the genera Hespellia, Ruminococcus and Clostridium were detected in samples from Austria, while those from genera Lysobacter, Staphylococcus and Clostridium were detected in samples from Belgium. Moreover, samples from France were characterized by Staphylococcus, Pseudomonas, and Hydrogenophilus genera. Finally, the genera Staphylococcus, Hydrogenophilus, Clostridium and Ruminococcus were identified in the samples produced in the Netherlands. When insects are intended for commercialization, rearing, processing and handling could affect the presence of the occurring microbial species. Hence, to assure a safe product, the need for a full standardization of production technologies, including feed supply as well as rearing and processing practices, is recommended.

Bacterial and Fungal Communities of Gioddu as Revealed by PCR–DGGE Analysis Abstract Gioddu is the sole variety of fermented milk originating in Italy. Despite the long history of consumption, Gioddu still represents an undisclosed source of microbial diversity. The present study was aimed to get an insight into the bacterial and fungal diversity of Gioddu samples collected from two artisan producers located in Sardinia. To this end 3 batches of Gioddu were collected from each producer and subjected to Polymerase Chain Reaction–Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analyses. Gioddu was produced with sheep milk in accordance with the local tradition. Regarding the bacterial population, a low biodiversity emerged. In more detail, the sole species Lactobacillus delbrueckii subsp. bulgaricus was detected in all the samples, irrespective of the producer or the batch. A more ample microbial diversity was highlighted for the fungal population that included closest relatives to Pichia cactophila, Kluyveromyces marxianus and Galactomyces candidum. Based on the results, the detected bacterial and fungal species generally clustered in accordance with the producer, irrespective of the batch considered. It is noteworthy that, Gioddu revealed several microbiological similarities with kefir beverage, thus suggesting, by analogy, potential health benefits related to its consumption. More research is needed to better clarify the microbiota composition of Gioddu by using more powerful metagenomic techniques.

Phomopsis tersa as Inhibitor of Quorum Sensing System and Biofilm Forming Ability of Pseudomonas aeruginosa Abstract Endophytic fungi provide rich reservoir for novel antimicrobial compounds. An endophytic fungus, from Carica papaya plant identified as Phomopsis tersa, was investigated for attenuating the quorum sensing mediated pathogenicity of Pseudomonas aeruginosa PAO1. Crude extract of P. tersa was found to reduce the production of redox-active pigments—pyocyanin and pyoverdine in P. aeruginosa PAO1 by 92.46% and 71.55%, respectively at sub-MIC concentration of 900 μg/mL. In addition, the crude extract was also able to inhibit the expression of virulence factors involved in biofilm formation: exopolysaccharide (72.21%) and alginate (72.50%). Secretion of cell-lytic enzymes was also found to be reduced: chitinase by 79.73% and elastase by 74.30%. 3-Isobutylhexahydropyrrolo[1,2-a]pyrazine-1,4-dione identified from GC-MS analysis, displayed favorable molecular interactions with P. aeruginosa transcriptional regulators, LasR and RhlR with good docking scores of − 6.873 kJ/mol and − 6.257 kJ/mol, respectively. The study thus reveals the potential use of P. tersa for discovering drugs against infectious pathogens.

Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade Abstract Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.

Recent Advancements in the Development of Modern Probiotics for Restoring Human Gut Microbiome Dysbiosis Abstract A healthy gut is predominantly occupied by bacteria which play a vital role in nutrition and health. Any change in normal gut homeostasis imposes gut dysbiosis. So far, efforts have been made to mitigate the gastrointestinal symptoms using modern day probiotics. The majority of the probiotics strains used currently belong to the genera Lactobacillus, Clostridium, Bifidobacterium and Streptococcus. Recent advancements in culturomics by implementing newer techniques coupled with the use of gnotobiotic animal models provide a subtle ground to develop novel host specific probiotics therapies. In this review article, the recent advances in the development of microbe-based therapies which can now be implemented to treat a wide spectrum of diseases have been discussed. However, these probiotics are not classified as drugs and there is a lack of stringent law enforcement to protect the end users against the pseudo-probiotic products. While modern probiotics hold strong promise for the future, more rigorous regulations are needed to develop genuine probiotic products and characterize novel probiotics using the latest research and technology. This article also highlights the possibility of reducing antibiotic usage by utilizing probiotics developed using the latest concepts of syn and ecobiotics.

Characterization and Application of a Robust Glucose Dehydrogenase from Paenibacillus pini for Cofactor Regeneration in Biocatalysis Abstract Glucose dehydrogenases are important auxiliary enzymes in biocatalysis, employed in the regeneration of reduced nicotinamide cofactors for oxidoreductase catalysed reactions. Here we report the identification and characterization of a novel glucose-1-dehydrogenase (GDH) from Paenibacillus pini that prefers NAD+ as cofactor over NADP+. The purified recombinant P. pini GDH displayed a specific activity of 247.5 U/mg. The enzyme was stable in the pH range 4–8.5 and exhibited excellent thermostability till 50 °C for 24 h, even in the absence of NaCl or glycerol. Paenibacillus pini GDH was also tolerant to organic solvents, demonstrating its potential for recycling cofactors for biotransformation. The potential application of the enzyme was evaluated by coupling with a NAD+-dependent alcohol dehydrogenase for the reduction of acetophenone and ethyl-4-chloro-3-oxo-butanoate. Conversions higher than 95% were achieved within 2 h with low enzyme loading using lyophilized cell lysate, suggesting that P. pini GDH could be highly effective for recycling NADH in redox biocatalysis.

Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome Abstract The term hygiene is deeply rooted with the concept of maintaining sound health and alertness towards cleanliness, while “hygiene hypothesis” depicts the protective role of microbial community exposure in development of early immunity and initial allergic and aesthetic reactions. The tug-of-war has now been pushed toward the literal term “hygiene” over the “hygiene hypothesis” and has continued with disinfection of all microbial loads from the related environments to avoid infections in humans. With the advancement in the microbiome studies, it became clear that humans possess warm, and significant relationships with diverse microbial community. With this opinion article, we have emphasized on the importance of hygiene hypothesis in immunological responses. We also propose the individual/targeted hygiene instead of application of unanimous hygiene hypothesis. This review also elaborates the common practices that should be employed to maintain hygiene along with the balanced microbiome.

Chicken Gut Microbiome and Human Health: Past Scenarios, Current Perspectives, and Futuristic Applications Abstract Sustainable poultry practices are needed to maintain an adequate supply of poultry products to the increasing human population without compromising human wellbeing. In order to achieve the understanding of the core microbiome that assumes an imperative role in digestion, absorption, and assimilation of feed as well as restrict the growth of pathogenic strains, a proper meta-data survey is required. The dysbiosis of the core microbiome or any external infection in chickens leads to huge losses in the poultry production worldwide. Along with this, the consumption of infected meat also impacts on human health as chicken meat is a regular staple in many diets as a vital source of protein. To tackle these losses, sub-therapeutic doses of antibiotics are being used as a feed additive along with other conventional approaches including selective breeding and modulation in feed composition. Altogether, these conventional approaches have improved the yield and quality of poultry products, however, the use of antibiotics encompasses the risk of developing multi-drug resistant pathogenic strains that can be harmful to human beings. Thus, there is an urgent need to understand the chicken microbiome in order to modulate chicken gut microbiome and provide alternatives to the conventional methods. Although there is now emerging literature available on some of these important microbiome aspects, in this article, we have analysed the relevant recent developments in understanding the chicken gut microbiome including the establishment of integrated gene catalogue for chicken microbiome. We have also focussed on novel strategies for the development of a chicken microbial library that can be used to develop novel microbial consortia as novel probiotics to improve the poultry meat production without compromising human health. Thus, it can be an alternative and advanced step compared to other conventional approaches to improve the gut milieu and pathogen-mediated loss in the poultry industry.

Interplay of Human Gut Microbiome in Health and Wellness Abstract The gut microbiome analysis, with specific interest on their direct impact towards the human health, is currently revolutionizing the unexplored frontiers of the pathogenesis and wellness. Although in-depth investigations of gut microbiome, ‘the Black Boxes’, complexities and functionalities are yet at its infancy, profound evidences are being reported for their concurrent involvement in disease etiology and its treatment. Interestingly, studies from the ‘minimal murine’ (Oligo-MM12), ‘humanized’ microbiota gnotobiotic mice models and patient samples, combined with multi-omics and cell biology approaches, have been revealing the implications of these findings in the treatment of gut dysbiosis associated diseases. Nonetheless, due to the inherent heterogeneity of the gut commensals and their unified co-existence with opportunistic pathobionts, it is utmost essential to highlight their functionalities in ‘good or bad’ gut in human wellness. We have specifically reviewed dietary lifestyle and infectious diseases linked with the gut bacterial consortia to delineate the ecobiotic approaches towards their treatment. This notably includes gut mucosal immunity mediated diseases such as Tuberculosis, IBD, CDI, Type 2 Diabetes, etc. Alongside of each dysbiosis, we have described the current therapeutic advancements of the pre- and probiotics derived from human microbiome studies to restore gut microbial homeostasis. With a continuous running debate on the role of microbiota in above mentioned diseases, we have collected numerous scientific evidences highlighting a previously unanticipated complex involvement of gut microbiome in the potential of human health.