Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics

Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities

(2019) Cresten Mansfeldt et al.   ISME Journal

Abundance and diversity of anammox bacteria in a mainstream municipal wastewater treatment plant

(2018) Ali Nejidat et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis

(2018) Jinqiu Xiao et al.   JOURNAL OF PROTEOME RESEARCH

Assessing the impact of protein extraction methods for human gut metaproteomics

(2018) Xu Zhang et al.   Journal of Proteomics

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

Aggregation ability of three phylogenetically distant anammox bacterial species

(2018) Muhammad Ali et al.   WATER RESEARCH

Genome-Centered Metagenomics Analysis Reveals the Symbiotic Organisms Possessing Ability to Cross-Feed with Anammox Bacteria in Anammox Consortia

(2018) Yunpeng Zhao et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure

(2017) Ananda S. Bhattacharjee et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

(2017) Lucas Moitinho-Silva et al.   ISME Journal

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

(2017) Jonathan D. Caranto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mainstream upflow nitritation-anammox system with hybrid anaerobic pretreatment: Long-term performance and microbial community dynamics

(2017) Xiaojin Li et al.   WATER RESEARCH

Microbial competition among anammox bacteria in nitrite-limited bioreactors

(2017) Lei Zhang et al.   WATER RESEARCH

Metabolic network analysis reveals microbial community interactions in anammox granules

(2017) Christopher E. Lawson et al.   Nature Communications

Metagenomic analysis of anammox communities in three different microbial aggregates

(2016) Jianhua Guo et al.   ENVIRONMENTAL MICROBIOLOGY

Beyond the Black Queen Hypothesis

(2016) Alix Mas et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Nitrogen removal by granular nitritation–anammox in an upflow membrane-aerated biofilm reactor

(2016) Xiaojin Li et al.   WATER RESEARCH

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

(2016) Daan R. Speth et al.   Nature Communications

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

(2016) Xu Zhang et al.   Microbiome

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm

(2015) Jeremy J. Barr et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Unraveling interactions in microbial communities - from co-cultures to microbiomes

(2015) Justin Tan et al.   JOURNAL OF MICROBIOLOGY

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Deterministic processes vary during community assembly for ecologically dissimilar taxa

(2015) Jeff R. Powell et al.   Nature Communications

Differentiation in the microbial ecology and activity of suspended and attached bacteria in a nitritation-anammox process

(2014) Hongkeun Park et al.   BIOTECHNOLOGY AND BIOENGINEERING

Microbial Community Composition and Ultrastructure of Granules from a Full-Scale Anammox Reactor

(2014) Graciela Gonzalez-Gil et al.   MICROBIAL ECOLOGY

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Metaproteomics: Evaluation of protein extraction from activated sludge

(2014) Susan Hove Hansen et al.   PROTEOMICS

Full-scale partial nitritation/anammox experiences – An application survey

(2014) Susanne Lackner et al.   WATER RESEARCH

Shotgun metagenomic data reveals significant abundance but low diversity of “Candidatus Scalindua” marine anammox bacteria in the Arabian Sea oxygen minimum zone

(2014) Laura Villanueva et al.   Frontiers in Microbiology

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

(2014) Puntipar Sonthiphand et al.   Frontiers in Microbiology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. J. Morris et al.   mBio

Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria

(2011) Harry R. Harhangi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The feasibility of using a two-stage autotrophic nitrogen removal process to treat sewage

(2011) Bin Ma et al.   BIORESOURCE TECHNOLOGY

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Molecular mechanism of anaerobic ammonium oxidation

(2011) Boran Kartal et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Nitrogen removal performance and microbial community analysis of an anaerobic up-flow granular bed anammox reactor

(2010) Sunja Cho et al.   CHEMOSPHERE

Function-specific response to depletion of microbial diversity

(2010) Hannes Peter et al.   ISME Journal

The biofilm matrix

(2010) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biochemistry and molecular biology of anammox bacteria

(2009) Mike S. M. Jetten et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Full-Scale Nitrogen Removal from Digester Liquid with Partial Nitritation and Anammox in One SBR

(2009) Adriano Joss et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The membrane bioreactor: A novel tool to grow anammox bacteria as free cells

(2008) Wouter R.L. van der Star et al.   BIOTECHNOLOGY AND BIOENGINEERING