Diversity within species: interpreting strains in microbiomes
341
TL;DR: This Review aims to clarify advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics, and guides the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
read more
Abstract: Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Biogeography: An Ecological and Evolutionary Approach.
TL;DR: The Engines of the Planet II:Evolution, the Source of Novelty as mentioned in this paper is a history of biogeography with a focus on plate tectonics and the evolution of life on the planet.
619
Prevotella diversity, niches and interactions with the human host
TL;DR: Segata et al. as discussed by the authors reviewed the diversity, prevalence and potential connection of Prevotella spp. in the human host, highlighting how genomic methods and analysis have improved and should further help in framing their ecological role.
444
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
B. J. Shapiro,Jonathan Friedman,Otto X. Cordero,Sarah P. Preheim,Sonia Timberlake,Gitta Szabó,Martin F. Polz,Eric J. Alm +7 more
- 01 Apr 2012
TL;DR: This paper showed that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: a few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations.
397
The Healthy Microbiome-What Is the Definition of a Healthy Gut Microbiome?
TL;DR: Use of microbiome-based biomarkers in diagnosis, prognosis, risk profiling, and precision therapy requires definition of a healthy microbiome in different populations, but to determine features of the intestinal microbiota associated with health, there need improved microbiome profiling technologies, with strain-level resolution.
264
Trophic Interactions and the Drivers of Microbial Community Assembly
TL;DR: It is argued that networks of trophic interactions, in which the metabolic excretions of one species are the primary resource for another, constitute the central drivers of microbial community assembly.
252
References
Horizontal gene transfer among genomes: The complexity hypothesis
TL;DR: It is proposed that a major factor in the more frequent horizontal transfer of operational genes is that informational genes are typically members of large, complex systems, whereas operational genes are not, thereby making horizontalTransfer of informational gene products less probable (the complexity hypothesis).
1.2K
A new genomic blueprint of the human gut microbiota
Alexandre Almeida,Alex L. Mitchell,Miguel Boland,Samuel C. Forster,Gregory B. Gloor,Aleksandra Tarkowska,Trevor D. Lawley,Robert D. Finn +7 more
TL;DR: The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
H. Bjørn Nielsen,Mathieu Almeida,Agnieszka S. Juncker,Simon Rasmussen,Junhua Li,Shinichi Sunagawa,Damian R. Plichta,Laurent Gautier,Anders Gorm Pedersen,Eric Pelletier,Ida Bonde,Trine Nielsen,Chaysavanh Manichanh,Manimozhiyan Arumugam,Jean-Michel Batto,Marcelo B Quintanilha dos Santos,Nikolaj Blom,Natalia Borruel,Kristoffer Sølvsten Burgdorf,Fouad Boumezbeur,Francesc Casellas,Joël Doré,Piotr Dworzynski,Francisco Guarner,Torben Hansen,Falk Hildebrand,Rolf Sommer Kaas,Sean Kennedy,Karsten Kristiansen,Jens Roat Kultima,Pierre Leonard,Florence Levenez,Ole Lund,Bouziane Moumen,Denis Le Paslier,Nicolas Pons,Oluf Pedersen,Edi Prifti,Junjie Qin,Jeroen Raes,Søren J. Sørensen,Julien Tap,Sebastian Tims,David W. Ussery,Takuji Yamada,Pierre Renault,Thomas Sicheritz-Pontén,Peer Bork,Jun Wang,Søren Brunak,S. Dusko Ehrlich +50 more
TL;DR: This work presents a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.
1.1K
Strains, functions and dynamics in the expanded Human Microbiome Project
Jason Lloyd-Price,Jason Lloyd-Price,Anup Mahurkar,Gholamali Rahnavard,Gholamali Rahnavard,Jonathan Crabtree,Joshua Orvis,A. Brantley Hall,Arthur Brady,Heather Huot Creasy,Carrie McCracken,Michelle G. Giglio,Daniel McDonald,Eric A. Franzosa,Eric A. Franzosa,Rob Knight,Owen White,Curtis Huttenhower,Curtis Huttenhower +18 more
TL;DR: A second wave of data from the National Institutes of Health Human Microbiome Project is introduced, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals to provide new characterizations of microbiome personalization.
Soft Sweeps: Molecular Population Genetics of Adaptation From Standing Genetic Variation
TL;DR: This work uses diffusion theory to calculate the probabilities for selective adaptations and finds a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation.