High-throughput microbial culturomics using automation and machine learning

High-throughput microbial culturomics using automation and machine learning

(2023) Yiming Huang et al.   NATURE BIOTECHNOLOGY

Elevated rates of horizontal gene transfer in the industrialized human microbiome

(2021) Mathieu Groussin et al.   CELL

The long-term genetic stability and individual specificity of the human gut microbiome

(2021) Lianmin Chen et al.   CELL

Regulation of colony morphology and biofilm formation in Shewanella algae

(2021) Alberto J. Martín‐Rodríguez et al.   Microbial Biotechnology

Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides

(2021) Lars J. Lindstad et al.   mBio

Macroecological dynamics of gut microbiota

(2020) Brian W. Ji et al.   Nature Microbiology

Co-Culture with Bifidobacterium catenulatum Improves the Growth, Gut Colonization, and Butyrate Production of Faecalibacterium prausnitzii: In Vitro and In Vivo Studies

(2020) Heejung Kim et al.   Microorganisms

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

(2020) William J Watterson et al.   eLife

Early detection and classification of live bacteria using time-lapse coherent imaging and deep learning

(2020) Hongda Wang et al.   Light-Science & Applications

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture

(2020) Max M. Villa et al.   mSystems

Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation

(2020) Laura C. Woods et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

(2019) Vivek K. Mutalik et al.   Nature Communications

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

Application of Machine Learning in Microbiology

(2019) Kaiyang Qu et al.   Frontiers in Microbiology

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

(2019) Brian W. Ji et al.   NATURE METHODS

A practical guide to intelligent image-activated cell sorting

(2019) Akihiro Isozaki et al.   Nature Protocols

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

(2019) Braden T. Tierney et al.   Cell Host & Microbe

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

The spatial and metabolic basis of colony size variation

(2018) Jeremy M. Chacón et al.   ISME Journal

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Modifying and reacting to the environmental pH can drive bacterial interactions

(2018) Christoph Ratzke et al.   PLOS BIOLOGY

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems

(2018) Clémence Defois et al.   Scientific Reports

Novel neural network application for bacterial colony classification

(2018) Lei Huang et al.   Theoretical Biology and Medical Modelling

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Colony-morphology screening uncovers a role for thePseudomonas aeruginosanitrogen-related phosphotransferase system in biofilm formation

(2015) Matthew T. Cabeen et al.   MOLECULAR MICROBIOLOGY

EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

(2015) Valerie Eichinger et al.   NUCLEIC ACIDS RESEARCH

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Emerging mass spectrometry techniques for the direct analysis of microbial colonies

(2014) Jinshu Fang et al.   CURRENT OPINION IN MICROBIOLOGY

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

(2014) Elizabeth A. Rettedal et al.   Nature Communications

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry

(2013) Nicole Strittmatter et al.   CHEMICAL COMMUNICATIONS

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene

(2009) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence

(2008) Mario Juhas et al.   CELLULAR MICROBIOLOGY