Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry

Boddu, Ramya Sree; Divakar, K.

doi:10.1007/978-981-10-7140-9_2

Cited by 5 publications

(3 citation statements)

References 77 publications

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“…A significant benefit is detection of microorganisms in water that were previously missed or not identified by culture-dependent methods [22,26,27]. Metagenomic surveys carried out by other investigators have provided evidence that ingested dietborne components can have short-and long-term effects on the human microbiota [28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis of drinking water employing metagenomics

et al. 2020

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The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.

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Section: Introductionmentioning

confidence: 99%

A comparative analysis of drinking water employing metagenomics

et al. 2020

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“…La metagenómica se refiere a un área de estudio que permite la extracción y el análisis de información genómica de microbiota no cultivada, es decir, de una muestra tomada del ambiente [34]. Esto resulta ventajoso sobre los métodos genómicos regulares debido a que no hay necesidad de hacer un cultivo de los microorganismos bajo condiciones controladas en el laboratorio [34].…”

Section: Metagenómica Y Procesos De Fermentaciónunclassified

Biología sintética en la ingenierización de rutas metabólicas de microorganismos para la obtención de compuestos de interés para la industria alimentaria

Ortuño-Fajardo

Chacón-Halabi

Flores-Espinoza

et al. 2021

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La ingeniería de rutas metabólicas, por medio de la biología sintética, se ha convertido en una herramienta de suma importancia para la industria alimentaria, debido a que se busca la optimización de procesos y obtención de compuestos ya existentes. Es posible producir compuestos que son altamente codiciados por el mercado, como enzimas que participan en procesos de fermentación o síntesis de productos de alta demanda, o saborizantes obtenidos de forma natural a partir de microorganismos modificados. Dicha edición genética se ha logrado mediante las técnicas desarrolladas en la rama de la biología sintética a lo largo de los años, como, por ejemplo, el ensamblaje de constructos genéticos y de CRISPR y ARN, mensajeros sintéticos. Estas técnicas son utilizadas para aumentar la productividad de un compuesto de interés en un microorganismo. No obstante, es necesario tomar en cuenta que no todos los microorganismos tienen las herramientas genéticas para realizar las modificaciones post-traduccionales necesarias para otorgar funcionalidad a una enzima o proteína, y que con una ruta metabólica de novo pueden producirse también compuestos e intermediarios tóxicos para el hospedero elegido. Particularmente, en la industria alimentaria es común la elección de microorganismos huéspedes que se consideren seguros para el consumo humano (GRAS) como las bacterias ácido-lácticas (LAB) y, más recientemente, las levaduras del género Saccharomyces.

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“…For example, microbiome studies on the human body have yielded an abundance of beneficial knowledge in the health and medical fields: diet [10], aging [11], obesity [12], diabetes [13], diseases of the digestive system [14], and so on. In the food and pharmaceutical industries, environmental microbiome studies have also been gathering attention for discovering novel valuable microorganisms [15]. Furthermore, plant microbiome studies have highlighted the relevance of the microbial community to crop productivity [16] and pathogen resistance [7].…”

Section: Introductionmentioning

confidence: 99%

Multivariate statistical monitoring system for microbial population dynamics

Ishiya¹,

Aburatani²

2021

Phys. Biol.

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Microbiomes in their natural environments vary dynamically with changing environmental conditions. The detection of these dynamic changes in microbial populations is critical for understanding the impact of environmental changes on the microbial community. Here, we propose a novel method to detect time-series changes in the microbiome, based on multivariate statistical process control. By focusing on the interspecies structures, this approach enables the robust detection of time-series changes in a microbiome composed of a large number of microbial species. Applying this approach to empirical human gut microbiome data, we accurately traced time-series changes in microbiota composition induced by a dietary intervention trial. This method was also excellent for tracking the recovery process after the intervention. Our approach can be useful for monitoring dynamic changes in complex microbial communities.

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Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry

Cited by 5 publications

References 77 publications

A comparative analysis of drinking water employing metagenomics

A comparative analysis of drinking water employing metagenomics

Biología sintética en la ingenierización de rutas metabólicas de microorganismos para la obtención de compuestos de interés para la industria alimentaria

Multivariate statistical monitoring system for microbial population dynamics

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