Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation

Warmer temperatures favor slower-growing bacteria in natural marine communities

(2023) Clare I. Abreu et al.   Science Advances

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

(2022) Tianjiao Dai et al.   Nature Communications

Bacterial species rarely work together

(2022) Jacob D. Palmer et al.   SCIENCE

Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism

(2022) Hani Pira et al.   Diversity-Basel

Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

(2022) Cheng Gao et al.   Nature Communications

Coupling effect of high temperature and thermophilic bacteria indirectly accelerates the humification process of municipal sludge in hyperthermophilic composting

(2022) Feng Ma et al.   PROCESS SAFETY AND ENVIRONMENTAL PROTECTION

Emergent phases of ecological diversity and dynamics mapped in microcosms

(2022) Jiliang Hu et al.   SCIENCE

Environmental stress destabilizes microbial networks

(2021) Damian J. Hernandez et al.   ISME Journal

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

(2021) Anthony Ortiz et al.   ISME Journal

Climate warming enhances microbial network complexity and stability

(2021) Mengting Maggie Yuan et al.   Nature Climate Change

Airborne and indigenous microbiomes co‐drive the rebound of antibiotic resistome during compost storage

(2021) Hanpeng Liao et al.   ENVIRONMENTAL MICROBIOLOGY

Warming reshaped the microbial hierarchical interactions

(2021) Yuqi Zhou et al.   GLOBAL CHANGE BIOLOGY

Obligate cross-feeding expands the metabolic niche of bacteria

(2021) Leonardo Oña et al.   Nature Ecology & Evolution

Additional strains acting as key microbes promoted composting process

(2021) Yuxiang Zhao et al.   CHEMOSPHERE

In vitro interaction network of a synthetic gut bacterial community

(2021) Anna S. Weiss et al.   ISME Journal

Positive interactions are common among culturable bacteria

(2021) Jared Kehe et al.   Science Advances

Higher temperatures generically favour slower-growing bacterial species in multispecies communities

(2020) Simon Lax et al.   Nature Ecology & Evolution

Sharing vitamins: Cobamides unveil microbial interactions

(2020) Olga M. Sokolovskaya et al.   SCIENCE

Bacteria and archaea on Earth and their abundance in biofilms

(2019) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

Global diversity and biogeography of bacterial communities in wastewater treatment plants

(2019) Linwei Wu et al.   Nature Microbiology

Toxicity drives facilitation between 4 bacterial species

(2019) Philippe Piccardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Acetate-Inducing Metabolic States Enhance Polyhydroxyalkanoate Production in Marine Purple Non-sulfur Bacteria Under Aerobic Conditions

(2019) Mieko Higuchi-Takeuchi et al.   Frontiers in Bioengineering and Biotechnology

Metagenomic and chemical characterization of soil cobalamin production

(2019) Xinda Lu et al.   ISME Journal

Deciphering microbial interactions in synthetic human gut microbiome communities

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

Ecology and evolution of metabolic cross-feeding interactions in bacteria

(2018) Glen D'Souza et al.   NATURAL PRODUCT REPORTS

Accumulation of NO2 -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the Eastern Tropical North Pacific

(2018) Katherine R. Heal et al.   Environmental Microbiology Reports

Abundance determines the functional role of bacterial phylotypes in complex communities

(2018) Damian W. Rivett et al.   Nature Microbiology

Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae

(2018) Matthew B. Cooper et al.   ISME Journal

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

(2018) Shuo Jiao et al.   Microbiome

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Guided cobamide biosynthesis for heterologous production of reductive dehalogenases

(2018) Torsten Schubert et al.   Microbial Biotechnology

Cohesion: a method for quantifying the connectivity of microbial communities

(2017) Cristina M Herren et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Two distinct pools of B12analogs reveal community interdependencies in the ocean

(2016) Katherine R. Heal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil?

(2016) Minna Männistö et al.   SOIL BIOLOGY & BIOCHEMISTRY

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

(2016) Yong-Guan Zhu et al.   Science Bulletin

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

The activated sludge ecosystem contains a core community of abundant organisms

(2015) Aaron M Saunders et al.   ISME Journal

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

High Throughput Profiling of Antibiotic Resistance Genes in Urban Park Soils with Reclaimed Water Irrigation

(2014) Feng-Hua Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant

(2014) Feng Ju et al.   ISME Journal

The importance of species sorting differs between habitat generalists and specialists in bacterial communities

(2013) Anna J. Székely et al.   FEMS MICROBIOLOGY ECOLOGY

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton

(2012) Erin M. Bertrand et al.   Frontiers in Microbiology

Light-dependent gene regulation by a coenzyme B12-based photoreceptor

(2011) J. M. Ortiz-Guerrero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS