A primer on metagenomics and next‐generation sequencing in fish gut microbiome research

2021 ◽  
Author(s):  
Tina Kollannoor Johny ◽  
Rinu Madhu Puthusseri ◽  
Sarita Ganapathy Bhat
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiome ◽  
Next Generation ◽  
Microbiome Research ◽  
Fish Gut ◽  
Generation Sequencing

scholarly journals Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10237
Author(s):  
Benjamin D. Gallo ◽  
John M. Farrell ◽  
Brian Leydet
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiota ◽  
Fish Species ◽  
Gut Microbiome ◽  
High Performance ◽  
Round Goby ◽  
Species Variation ◽  
Next Generation ◽  
Fish Gut ◽  
Generation Sequencing

Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.

A new view of the fish gut microbiome: Advances from next-generation sequencing

Aquaculture ◽  
2015 ◽  
Vol 448 ◽  
pp. 464-475 ◽  
Author(s):  
Mahdi Ghanbari ◽  
Wolfgang Kneifel ◽  
Konrad J. Domig
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiome ◽  
Next Generation ◽  
Fish Gut ◽  
Generation Sequencing ◽  
New View

MICROBIOMA: AMIGO O ENEMIGO EN PACIENTES CON COVID - 19

SCIENTIARVM ◽  
2015 ◽  
Vol 1 (1) ◽  
pp. 15-21
Author(s):  
Katherine Milagros Quispe Medina ◽  
◽  
Angel Sixto Mamani Ruelas ◽  
Brenda Jasmin Alvarez Vera ◽  
Yasmin Yessenia Silvestre Gutierrez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Tract ◽  
Molecular Biology ◽  
Gut Microbiome ◽  
Next Generation ◽  
Multiple Factors ◽  
Lung Microbiome ◽  
The Relationship ◽  
Generation Sequencing ◽  
Clinical Cases

The research of the microbiome concerning various diseases has grown in the last ten years due to the advances in molecular biology and next-generation sequencing, finding interactions with various pathologies. The new coronavirus 19 (SARS-COV 2) pandemic has aroused interest in the study of multiple factors that could influence in the development of symptoms mainly due to the interaction of the microbiome whether of the respiratory or gastrointestinal tract finally in the prognosis. Therefore, in this study, we focus on reviewing and analyzing the current bibliography of research and clinical cases about the relationship between the lung and gut microbiome and COVID-19, highlighting its effect on infected patients, aiming to contribute to this new line of research. Keywords: Microbiome, COVID-19, SARS-COV 2, gut microbiome, lung microbiome.

Impact of Diet and the Gut Microbiome on Neurodegeneration and Regeneration in Neurological Disorders

Neuroforum ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 39-47
Author(s):  
Barbara Gisevius ◽  
Aiden Haghikia ◽  
Sarah Hirschberg
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiome ◽  
Neurological Disorders ◽  
Next Generation ◽  
Generation Sequencing

Zusammenfassung Aktuelle Forschungsergebnisse im Bereich neurodegenerativer Erkrankungen deuten vermehrt darauf hin, dass die Ernährung und damit assoziiert die Zusammensetzung des Darm-Mikrobioms einen entscheidenden Einfluss auf die Entstehung und den Verlauf verschiedenster Krankheiten haben. Die sogenannte Darm-Hirn Achse, oder präziser die Darm-Mikrobiom-Hirn Achse hat dadurch deutlich an Aufmerksamkeit gewonnen. Dabei kann der Darm das zentrale Nervensystem auf unterschiedliche Weisen beeinflussen, I) direkt durch bakterielle Bestandteile und Metaboliten von Bakterien, II) durch Manipulation der im Körper zirkulierenden Immunzellen, oder III) durch direkten Kontakt, z. B. über den N. vagus. Fortschritte auf dem Gebiet der Molekularbiologie, wie das Next Generation Sequencing ermöglichen aufgrund ihres hohen Auflösungsvermögens die genaue Identifikation von Bakterien und die Kompositionen ganzer Mikrobiome. Dadurch ist es möglich, die Interaktionen zwischen dem intestinalen Mikrobiom, dem Metabolom und dem Darm- assoziierten Immunsystem detailliert zu erforschen. In dieser Arbeit diskutieren wir den Einfluss des Mikrobioms, der Ernährung und den damit verbundenen Gesundheitszustand auf die Neuroregeneration. Der Fokus liegt dabei auf der Möglichkeit, wie dieses Wissen in Zukunft für therapeutische Zwecke genutzt werden kann.

scholarly journals Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation

2019 ◽  
Vol 15 ◽  
pp. 117693431984843 ◽  
Author(s):  
Ran Yao ◽  
Lianglaing Xu ◽  
Guoqing Lu ◽  
Lifeng Zhu
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiome ◽  
Environmental Changes ◽  
Next Generation ◽  
Evolutionary Potential ◽  
Animal Conservation ◽  
Père David’S Deer ◽  
Fresh Feces ◽  
Gut Microbial Community ◽  
Generation Sequencing

The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David’s deer ( Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.

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