An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

Gao, Bei; Chi, Liang; Zhu, Yixin; Shi, Xiaochun; Tu, Pengcheng; Li, Bing; Yin, Jun; Gao, Nan; Shen, Weishou; Schnabl, Bernd

doi:10.3390/biom11040530

Cited by 78 publications

(66 citation statements)

References 144 publications

(124 reference statements)

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“… 85 Compared with target sequence, metagenomics reads might be decreased biases from primer choices and increased community taxonomic characterization providing information of gene composition and the function. 86 …”

Section: Methods To Characterize the Gut Mycobiomementioning

confidence: 99%

The role of gut mycobiome in health and diseases

Zhang

Zhan

et al. 2021

Therap Adv Gastroenterol

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The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut “mycobiome”) play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.

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Section: Methods To Characterize the Gut Mycobiomementioning

confidence: 99%

The role of gut mycobiome in health and diseases

Zhang

Zhan

et al. 2021

Therap Adv Gastroenterol

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“…Usually, the gut microbiome engages in mutualistic relationships with the host, whereas it may mediate the occurrence and development of some diseases, which depends on both environment and the susceptibility of the host. Due to next generation sequencing technologies, such as 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and virome sequencing, identifying the characterization of host-microbiota interactions has tremendous progress and the intestinal microbiota is indicated to be closely related to CRC ( 5 , 6 ). The proposed pathogens which are candidates for CRC mainly include Fusobacterium nucleatum , Escherichia coli, Bacteroides fragilis , Streptococcus bovis , Enterococcus faecalis and Peptostreptococcus anaerobius ( 7 ).…”

Section: Introductionmentioning

confidence: 99%

Gut Microbiota-Derived Metabolites in Colorectal Cancer: The Bad and the Challenges

Zhang

Qin

et al. 2021

Front. Oncol.

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Accumulating evidence from studies in humans and animal models has elucidated that gut microbiota, acting as a complex ecosystem, contributes critically to colorectal cancer (CRC). The potential mechanisms often reported emphasize the vital role of carcinogenic activities of specific pathogens, but in fact, a series of metabolites produced from exogenous dietary substrates or endogenous host compounds occupy a decisive position similarly. Detrimental gut microbiota-derived metabolites such as trimethylamine-N-oxide, secondary bile acids, hydrogen sulfide and N-nitroso compounds could reconstruct the ecological composition and metabolic activity of intestinal microorganisms and formulate a microenvironment that opens susceptibility to carcinogenic stimuli. They are implicated in the occurrence, progression and metastasis of CRC through different mechanisms, including inducing inflammation and DNA damage, activating tumorigenic signaling pathways and regulating tumor immunity. In this review, we mainly summarized the intimate relationship between detrimental gut microbiota-derived metabolites and CRC, and updated the current knowledge about detrimental metabolites in CRC pathogenesis. Then, multiple interventions targeting these metabolites for CRC management were critically reviewed, including diet modulation, probiotics/prebiotics, fecal microbiota transplantation, as well as more precise measures such as engineered bacteria, phage therapy and chemopreventive drugs. A better understanding of the interplay between detrimental microbial metabolites and CRC would hold great promise against CRC.

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“…The most widely used method for sequencing the fecal microbiome thus far is 16S rRNA sequencing [ 62 ]. This sequencing method utilizes PCR to target and amplify portions of the hypervariable regions (V1–V9) of the bacterial 16S ribosomal RNA subunit gene.…”

Section: Discussionmentioning

confidence: 99%

“…This sequencing method utilizes PCR to target and amplify portions of the hypervariable regions (V1–V9) of the bacterial 16S ribosomal RNA subunit gene. In this way the method can differentiate between different bacterial organisms, as the 16S ribosomal RNA subunit gene contains two regions that are conserved throughout all bacterial species while the V1-V9 regions are unique for each genus [ 62 ]. Both the studies reviewed here [ 47 , 61 ], performed 16S rRNA sequencing of the hyper variable regions V3-V4 on the Illumina Miseq platform, but their methodological approaches diverged thereafter: Costabile et al utilized the mare package in R (Korpela 2016 mare: Microbiota Analysis in R Easily.…”

Section: Discussionmentioning

confidence: 99%

The Effect of Probiotics on Health Outcomes in the Elderly: A Systematic Review of Randomized, Placebo-Controlled Studies

et al. 2021

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Increasing evidence suggests that probiotic supplementation may be efficacious in counteracting age-related shifts in gut microbiota composition and diversity, thereby impacting health outcomes and promoting healthy aging. However, randomized controlled trials (RCTs) with probiotics in healthy older adults have utilized a wide variety of strains and focused on several different outcomes with conflicting results. Therefore, a systematic review was conducted to determine which outcomes have been investigated in randomized controlled trials with probiotic supplementation in healthy older adults and what has been the effect of these interventions. For inclusion, studies reporting on randomized controlled trials with probiotic and synbiotic supplements in healthy older adults (defined as minimum age of 60 years) were considered. Studies reporting clinical trials in specific patient groups or unhealthy participants were excluded. In addition to assessment of eligibility and data extraction, each study was examined for risk of bias and quality assessment was performed by two independent reviewers. Due to the heterogeneity of outcomes, strains, study design, duration, and methodology, we did not perform any meta-analyses and instead provided a narrative overview of the outcomes examined. Of 1997 potentially eligible publications, 17 studies were included in this review. The risk of bias was low, although several studies failed to adequately describe random sequence generation, allocation concealment, and blinding. The overall study quality was high; however, many studies did not include sample calculations, and the majority of studies had a small sample size. The main outcomes examined in the trials included microbiota composition, immune-related measurements, digestive health, general well-being, cognitive function, and lipid and other biomarkers. The most commonly assessed outcome with the most consistent effect was microbiota composition; all but one study with this outcome showed significant effects on gut microbiota composition in healthy older adults. Overall, probiotic supplementation had modest effects on markers of humoral immunity, immune cell population levels and activity, as well as the incidence and duration of the common cold and other infections with some conflicting results. Digestive health, general-well-being, cognitive function, and lipid and other biomarkers were investigated in a very small number of studies; therefore, the impact on these outcomes remains inconclusive. Probiotics appear to be efficacious in modifying gut microbiota composition in healthy older adults and have moderate effects on immune function. However, the effect of probiotic supplementation on other health outcomes remains inconclusive, highlighting the need for more well-designed, sufficiently-powered studies to investigate if and the mechanisms by which probiotics impact healthy aging.

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An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

Cited by 78 publications

References 144 publications

The role of gut mycobiome in health and diseases

The role of gut mycobiome in health and diseases

Gut Microbiota-Derived Metabolites in Colorectal Cancer: The Bad and the Challenges

The Effect of Probiotics on Health Outcomes in the Elderly: A Systematic Review of Randomized, Placebo-Controlled Studies

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