scholarly journals Optimisation of Sample Storage and DNA Extraction for Human Gut Microbiome Studies

2021 ◽  
Author(s):  
Jekaterina Kazantseva ◽  
Esther Malv ◽  
Aleksei Kaleda ◽  
Aili Kallastu ◽  
Anne Meikas
Keyword(s):  
Gut Microbiome ◽  
Personalised Medicine ◽  
Metagenomic Analysis ◽  
Human Gut ◽  
Health And Wellbeing ◽  
Sequencing Technologies ◽  
Different Temperatures ◽  
Stool Samples ◽  
Commercial Kits ◽  
Systemic Understanding

Abstract Background: New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiome studies, where all details and interactions between processes are important. Results: Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the metagenomic analysis of the human gut. Two commercial kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield preservation reagent proved to be a trustworthy solution for stool samples collection and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusion: Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

scholarly journals Optimisation of Sample Storage and DNA Extraction for Human Gut Microbiome Studies

2020 ◽  
Author(s):  
Jekaterina Kazantseva ◽  
Esther Malv ◽  
Aleksei Kaleda ◽  
Aili Kallastu ◽  
Anne Meikas
Keyword(s):  
Gut Microbiome ◽  
Personalised Medicine ◽  
Metagenomic Analysis ◽  
Human Gut ◽  
Health And Wellbeing ◽  
Sequencing Technologies ◽  
Different Temperatures ◽  
Stool Samples ◽  
Commercial Kits ◽  
Systemic Understanding

Abstract Background: New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiome studies, where all details and interactions between processes are important. Results: Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the metagenomic analysis of the human gut. Two commercial kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield preservation reagent proved to be a trustworthy solution for stool samples collection and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusion: Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

scholarly journals Optimisation of sample storage and DNA extraction for human gut microbiota studies​

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jekaterina Kazantseva ◽  
Esther Malv ◽  
Aleksei Kaleda ◽  
Aili Kallastu ◽  
Anne Meikas
Keyword(s):  
Gut Microbiota ◽  
Dna Extraction ◽  
Personalised Medicine ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Sequencing Technologies ◽  
Different Temperatures ◽  
Reliable Solution

Abstract Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

scholarly journals Taxonomic signatures of cause-specific mortality risk in human gut microbiome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aaro Salosensaari ◽  
Ville Laitinen ◽  
Aki S. Havulinna ◽  
Guillaume Meric ◽  
Susan Cheng ◽  
...  
Keyword(s):  
Mortality Risk ◽  
Gut Microbiome ◽  
Human Gut ◽  
Cross Sectional ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Non Invasive ◽  
Sequencing Technologies

AbstractThe collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

scholarly journals Gut Microbiome Alteration of Cold-adapated Antarctic copepod Tigriopus kingsejongensis with Temperature Changes and Developmental Stages

2021 ◽  
Author(s):  
Han Na Oh ◽  
Myeong Nu Ri ◽  
Taeyune Kim ◽  
Gi-Sik Min ◽  
Sanghee Kim ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Gut Microbiome ◽  
Developmental Stages ◽  
Glycosyl Hydrolase ◽  
Food Resource ◽  
Temperature Sensitive ◽  
Temperature Changes ◽  
Aquatic Microbes ◽  
Different Temperatures ◽  
Stool Samples

Abstract Tigriopus kingsejongensis, a copepod species, reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. Some copepods were temperature-sensitive in growth and post-embryonic development. We cultured T. kingsejongensis at three different temperatures (2°C, 8°C, and 15°C) in a laboratory to observe the alterations in the stool microbiome of copepods depending on the cultivation temperature and developmental stages. We observed copepod gut microbiome changes by increasing temperatures: a lower microbial diversity, a higher abundance of aquatic microbes, Vibrio, and a lower abundance of the psychrophilic microbes, Colwellia. Also, the copepod gut microbiome, according to the developmental stage, was changed: a lower microbial diversity in egg-attached copepods than nauplius at 8°C. We further analyzed three shotgun metagenomes from T. kingsejongensis stool samples at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolase (GHs) encoding chitinases and virulence factors with higher relative abundance at 15°C than at lower temperatures. These results that temperature and developmental stages affect the gut microbiome of copepods are helpful to understand the changes in the low-temperature adapted copepod with climate change.

scholarly journals Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 46 ◽  
Author(s):  
Brian V Jones ◽  
Funing Sun ◽  
Julian R Marchesi
Keyword(s):  
Gut Microbiome ◽  
Metagenomic Analysis ◽  
Human Gut ◽  
Human Gut Microbiome

What is the role of cyclic di-GMP signaling within the human gut microbiome?

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Rachel M. Rudlaff ◽  
Christopher M. Waters
Keyword(s):  
Gut Microbiome ◽  
Diguanylate Cyclase ◽  
Human Gut ◽  
Base Pairs ◽  
Metagenomic Dna ◽  
Human Gut Microbiome ◽  
Commensal Species ◽  
Stool Samples ◽  
Specific Species

AbstractThere is currently little understanding of the role of the bacterial second messenger cyclic di-GMP (c-di-GMP) in the human gut microbiome. C-di-GMP is synthesized by highly conserved diguanylate cyclase (DGC) enzymes and degraded by highly conserved phosphodiesterase (PDE) enzymes. To begin to assess the prevalence of c-di-GMP signaling in the gut microbiome, we found on average 1.0 DGC and 0.8 PDE enzymes per million base pairs of metagenomic DNA derived from stool samples. Specific species encoding substantial numbers of GGDEF and EAL domains were the commensal species

scholarly journals The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

2009 ◽  
Vol 1 (6) ◽  
pp. 6ra14-6ra14 ◽  
Author(s):  
P. J. Turnbaugh ◽  
V. K. Ridaura ◽  
J. J. Faith ◽  
F. E. Rey ◽  
R. Knight ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Metagenomic Analysis ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Gnotobiotic Mice
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