Metagenomics: a path to understanding the gut microbiome

Yen, Sandi; Johnson, Jethro

doi:10.1007/s00335-021-09889-x

Cited by 40 publications

(19 citation statements)

References 126 publications

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“…Microbiome characterization is generally based on three key techniques: (i) ribosomal RNA (rRNA) analysis, generally assisted by PCR amplification, (ii) DNA-based metagenomics, and (iii) RNA-seq combined with informatic analysis (reviewed in [ 16 – 23 ]), although several hybrid methods have been used. In the first, rRNA (or rDNA) sequences are amplified using a suite of PCR primers, sequenced, and compared against the database.…”

Section: Introductionmentioning

confidence: 99%

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

Haas

Lathe

2022

BMC Microbiol

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Background Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life. Results We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved. Conclusions This generic methodology is likely to find wide application in microbiome analysis including diagnostics.

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Section: Introductionmentioning

confidence: 99%

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

Haas

Lathe

2022

BMC Microbiol

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“…Metagenomics is an analysis of the entire genetic material of microbiota in the living environment and is an important way to understand the taxonomic and functional characterization of intestinal microbiota [ 29 ]. General gut microbes of animals have been called the second genome of individuals, and there is growing evidence that microbial components are correlated with host genetics [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake

Zhou

Yang

et al. 2023

Microorganisms

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Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.

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“…Reliable and meaningful scientific conclusions from microbiome studies rely on accurate analysis of microbial communities [249]. Several recent publications have discussed procedures for overcoming threats to reproducibility, replicability, robustness, and generalizability in microbiome research [250][251][252][253][254].…”

Section: Quantitative Assessment Of Transmission Of Microbiotamentioning

confidence: 99%

Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations

Rosenberg

Zilber‐Rosenberg

2021

Microorganisms

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Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism’s microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.

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Metagenomics: a path to understanding the gut microbiome

Cited by 40 publications

References 126 publications

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake

Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations

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