Sequencing and beyond: integrating molecular ‘omics for microbial community profiling

By Eric A. Franzosa, T. Hsu, Alexandra Sirota-Madi, Afrah Shafquat, Galeb Abu-Ali, Xochitl C. Morgan, Curtis Huttenhower. 2015

628 citations recorded by the source corpus.

High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring multiple 'omic' data types that better capture community functional activity, such as transcriptomics, proteomics and metabolomics; and combining multiple forms of omic data in an integrated framework. We highlight studies in which the 'multi-omics' approach has led to improved mechanistic models of microbial community structure and function.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

MMseqs2: sensitive protein sequence searching for the analysis of massive data sets (2017, methodology): “of sequences are being performed, such as the genome 10K project [11] and metagenomic and metatranscriptomic studies with applications in medical, biotechnological, microbiological, and agricultural research [1, 3, 8, 13, 25].”
Gut microbiota functions: metabolism of nutrients and other food components (2017, background): “Meta-omic analyses have resulted in a tremendous amount of data on the composition, encoded functionalities, and metabolic output of the human gut microbiota [135].”
The Human Gut Microbiome: From Association to Modulation. (2018, neutral): “More recently, however, the taxonomic and functional census 695 provided by metagenomics is increasingly complemented by readouts on activity, provided by 696 metatranscriptomics, metaproteomics and metabolomics (reviewed by Franzosa et al., 2015; 697 Mallick et al., 2017).”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, background): “Together, these studies promise to provide a highresolution picture of bacteria-host interactions that may lead to disease (Franzosa et al., 2015).”
Insights into Cronobacter sakazakii Biofilm Formation and Control Strategies in the Food Industry (2020, background): “This is primarily due to advances in DNA sequencing, which is now invaluable for probing microbial community composition and function in diverse environments at high resolution [68].”
Multivariable association discovery in population-scale meta-omics studies (2021, background): “, nonbacterial, metagenomic, metatranscriptomic, metabolomic, and metaproteomic measurements assessed simultaneously in the same biological specimens [3,4].”
A review of methods and databases for metagenomic classification and assembly (2019, background): “Integrating the data of all these different ‘meta-omics’ approaches is challenging, but it can yield insights not found by looking at just one type of data [7].”
Human gut microbiome: hopes, threats and promises (2018, background): “66 Several interesting studies have also proposed that the micro-biome should be seen as an integral part of precision medicine approach (for review see Suez and Elinav and Kashyap et al 67 68 ) because it contributes to interindividual variability in all aspects of diseases situation but is also a…”
Species-level functional profiling of metagenomes and metatranscriptomes (2018, neutral): “We further benchmarked the performance of tiered search on 397 HMP metagenomes spanning six body sites (Supplementary Note 4).”