Microbiota Analysis Using an Illumina MiSeq Platform to Sequence 16S rRNA Genes

Rapin, Alexis; Pattaroni, Céline; Marsland, Benjamin J.; Harris, Nicola L.

doi:10.1002/cpmo.29

Cited by 40 publications

(25 citation statements)

References 35 publications

(46 reference statements)

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“…In order to study the impact of age-related changes of microbiota on lipid homeostasis, we transferred the fecal microbiota of young vs. old donor mice into germ-free mice. The composition of the fecal microbiota recovered in mice after 2 months of colonization was analyzed by 16S rRNA gene sequencing, a powerful tool widely used to explore the composition of bacterial communities (Rapin et al, 2017). We showed that microbiota were different between the two groups of mice, with that of mice inoculated with fecal microbiota of old donors recapitulating some features described in the elderly.…”

Section: Discussionmentioning

confidence: 99%

“…This includes an increase in the relative abundance of Escherichia-Shigella, a bacterial genus associated with inflammation, and a decrease in Christensenellaceae, a bacterial family associated with longevity (Biagi et al, 2016;Kumar et al, 2016). However, it should be noticed that the 16S rRNA sequencing method has some limitations and gives little information about the whole genetic, functional, and metabolic capabilities of the microbiota (Rapin et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

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Age-Related Changes in the Gut Microbiota Modify Brain Lipid Composition

Albouery

Buteau

Grégoire

et al. 2020

Front. Cell. Infect. Microbiol.

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Understanding the molecular mechanisms underlying the changes observed during aging is a prerequisite to design strategies to prevent age-related diseases. Aging is associated with metabolic changes, including alteration in the brain lipid metabolism. These alterations may contribute to the development of pathophysiological conditions. Modifications in the gut microbiota composition are also observed during aging. As communication axes exist between the gut microbiota and the brain and knowing that microbiota influences the host metabolism, we speculated on whether age-associated modifications in the gut microbiota could be involved in the lipid changes observed in aging brain. For that purpose, germ-free mice were colonized by the fecal microbiota of young or old donor mice. Lipid classes and fatty acid profiles were determined in the brain (cortex), plasma and liver by thin-layer chromatography on silica gel-coated quartz rods and gas chromatography. Gut colonization by microbiota of old mice resulted in a significant increase in total monounsaturated fatty acids (MUFA) and a significant decrease in the relative amounts of cholesterol and total polyunsaturated fatty acids (PUFA) in the cortex. Among the eight most represented fatty acids in the cortex, the relative abundances of five (C18:1n-9, C22:6n-3, C20:4n-6, C18:1n-7, and C20:1n-9) were significantly altered in mice inoculated with an aged microbiota. Liquid chromatography analyses revealed that the relative abundance of major species among phosphatidyl and plasmenylcholine (PC 16:0/18:1), phosphatidyl and plasmenylethanolamine (PE 18:0/22:6), lysophosphatidylethanolamine (LPE 22:6) and sphingomyelins (SM d18:1/18:0) were significantly altered in the cortex of mice colonized by the microbiota obtained from aged donors. Transplantation of microbiota from old mice also modified the lipid class and fatty acid content in the liver. Finally, we found that the expression of several genes involved in MUFA and PUFA synthesis (Scd1, Fads1, Fads2, Elovl2, and Elovl5) was dysregulated in mice inoculated with an Albouery et al.Microbiota Modulates Brain Lipid Composition aged microbiota. In conclusion, our data suggest that changes in gut microbiota that are associated with aging can impact brain and liver lipid metabolisms. Lipid changes induced by an aged microbiota recapitulate some features of aging, thus pointing out the potential role of microbiota alterations in the age-related degradation of the health status.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Age-Related Changes in the Gut Microbiota Modify Brain Lipid Composition

Albouery

Buteau

Grégoire

et al. 2020

Front. Cell. Infect. Microbiol.

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“…With the development of new technology, the application of whole genome sequencing (WGS) allows access to all genes of virtually all inflammation with dysbiosis of skin microbiota. Next-generation sequencing (NGS) technology in clinical bacteriology has been interrogating thousands of 16S ribosomal RNA gene amplicons from bacteria to archaea in floras from a patient with AD [8,9]. Currently, exploration of the skin microbiome in AD is attracting more and more attention from researchers.…”

Section: Introductionmentioning

confidence: 99%

A Calm, Dispassionate Look at Skin Microbiota in Atopic Dermatitis: An Integrative Literature Review

Wan

Chen

2020

Dermatol Ther (Heidelb)

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Atopic dermatitis (AD) is a chronic common inflammatory skin disorder with clinical characteristics of pruritic, dry, and recurrent flares that involve the whole body. Recent studies have demonstrated that the skin microbiota, characterized by an overgrowth of Staphylococcus aureus (S. aureus), plays a critical role in the manifestation of AD. There is striking evidence that skin microbiota can modulate the development and progression of AD. Therefore, more and more therapeutic approaches are adopted for modifying skin microbiota. Here we discuss the role of skin microbiota in the etiology and maintenance of AD; furthermore, we summarize the effects of therapeutic treatments on skin microbiota in AD based on published literature. With the help of the theoretical guidance suggested by microbial metagenome analysis, the reconstitution of microbiota should be a promising way to harness the pathogens of AD and could be used as a brandnew therapeutic strategy in clinical trials. We believe that the targeted therapy of dysbiosis in AD may possibly become a unique approach to an integrated treatment program in the near future.

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“…Bacterial communities were assessed by high-throughput sequencing of the v1-v2 hyper-variable regions of the bacterial 16S rRNA gene as previously described ((28), following the basic protocol “Bacterial 16S rRNA sequencing for bacterial communities present in intestinal contents of mice, or from fecal samples collected from mice or humans”). Samples were processed in nine sequencing runs on an Illumina MiSeq platform using Paired End (PE) v2 2×250 chemistry.…”

Section: Methodsmentioning

confidence: 99%

Infection with a small intestinal helminth Heligmosomoides polygyrus bakeri consistently alters microbial communities throughout the small and large intestine

Harris

Rapin²,

Chuat

et al. 2019

Preprint

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Increasing evidence suggests that intestinal helminth infection can alter intestinal microbial communities with important impacts on the mammalian host. However, all of the studies to date utilize different techniques to study the microbiome and access different sites of the intestine with little consistency noted between studies. In the present study, we set out to perform a comprehensive analysis of the impact of intestinal helminth infection on the mammalian intestinal bacterial microbiome. For this purpose, we investigated the impact of experimental infection using the natural murine small intestinal helminth, Heligmosomoides polygyrus bakeri (Hpb) and examined possible alterations in both the mucous and luminal bacterial communities along the entire small and large intestine. We also explored the impact of common experimental variables, including the parasite batch and pre-infection microbiome, on the outcome of helminth-bacterial interactions. This work provides evidence that helminth infection reproducibly alters intestinal microbial communities – with an impact of infection noted along the entire length of the intestine. Although the exact nature of helminth-induced alterations to the intestinal microbiome differed depending on the parasite batch and microbiome community structure present prior to infection, changes extended well beyond the introduction of new bacterial species by the infecting larvae. Moreover, striking similarities between different experiments were noted, including the consistent outgrowth of a bacterium belonging to the Peptostreptococcaceae family throughout the intestine. Author Summary Increasing evidence indicates a role for interactions between intestinal helminths and the microbiome in regulating mammalian health, and a greater understanding of helminth-microbiota interactions may open the path for the development of novel immunomodulatory therapies. However, such studies are hampered by the inconsistent nature of the data reported so far. Such inconsistancies likely result from variations in the experimental and technological methodologies employed to investigate helminth-microbiota interactions and well has natural variation in the starting microbiome composition and/or worm genetics. We conducted a thorough study in which the reproducibility of helminth-induced alterations of microbial communities was determined and impact of common experimental variables – such as the starting microbiome and parasite batch - was determined. Our work reveals the robust ability of small intestinal helminth infection to alter microbial communities along the entire length of the intestine and additionally identifies a single bacterium that is strongly associated with infection across multiple experiments.

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Microbiota Analysis Using an Illumina MiSeq Platform to Sequence 16S rRNA Genes

Cited by 40 publications

References 35 publications

Age-Related Changes in the Gut Microbiota Modify Brain Lipid Composition

Age-Related Changes in the Gut Microbiota Modify Brain Lipid Composition

A Calm, Dispassionate Look at Skin Microbiota in Atopic Dermatitis: An Integrative Literature Review

Infection with a small intestinal helminth Heligmosomoides polygyrus bakeri consistently alters microbial communities throughout the small and large intestine

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