Predicting measures of soil health using the microbiome and supervised machine learning

Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

(2021) Roland C. Wilhelm et al.   mBio

Effects of plant community history, soil legacy and plant diversity on soil microbial communities

(2021) Marc W. Schmid et al.   JOURNAL OF ECOLOGY

Long‐term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions

(2021) Florian Gschwend et al.   MOLECULAR ECOLOGY

Linking microbial taxa and the effect of mineral nitrogen forms on residue decomposition at the early stage in arable soil by DNA-qSIP

(2021) Weiling Dong et al.   GEODERMA

Introducing the North American project to evaluate soil health measurements

(2020) Charlotte E. Norris et al.   AGRONOMY JOURNAL

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils

(2020) Anastasia A. Ivanova et al.   PLoS One

Using soil bacterial communities to predict physico-chemical variables and soil quality

(2020) Syrie M. Hermans et al.   Microbiome

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

(2020) Marie J. Zwetsloot et al.   SOIL BIOLOGY & BIOCHEMISTRY

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

(2020) Begüm D. Topçuoğlu et al.   mBio

Soil Health Gap: A concept to establish a benchmark for soil health management

(2020) Bijesh Maharjan et al.   Global Ecology and Conservation

The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities

(2019) Jennifer D. Rocca et al.   Frontiers in Microbiology

Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation

(2019) Liangliang Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Soil health characterization in smallholder agricultural catchments in India

(2019) Phillip S.D. Frost et al.   APPLIED SOIL ECOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition

(2019) Jaron Thompson et al.   PLoS One

Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

(2019) Marc A. Sze et al.   mBio

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

(2019) Yi-Hui Zhou et al.   Frontiers in Genetics

Legacy effects of contrasting organic grain cropping systems on soil health indicators, soil invertebrates, weeds, and crop yield

(2019) Ashley B. Jernigan et al.   AGRICULTURAL SYSTEMS

Microbial indicators are better predictors of wheat yield and quality than N fertilization

(2019) Étienne Yergeau et al.   FEMS MICROBIOLOGY ECOLOGY

The influence of soil management on soil health: An on-farm study in southern Sweden

(2019) Hanna Williams et al.   GEODERMA

No-till and cropping system diversification improve soil health and crop yield

(2018) Márcio Renato Nunes et al.   GEODERMA

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Plant Growth-Promoting Rhizobacteria (PGPR) Reduce Evaporation and Increase Soil Water Retention

(2018) Wenjuan Zheng et al.   WATER RESOURCES RESEARCH

Soil quality change 50 years after forestland conversion to tea farming

(2018) Azadeh Gholoubi et al.   Soil Research

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

(2018) Li Chen et al.   PeerJ

Soil health assessment: A critical review of current methodologies and a proposed new approach

(2018) Oshri Rinot et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Methods for normalizing microbiome data: an ecological perspective

(2018) Donald T. McKnight et al.   Methods in Ecology and Evolution

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities

(2017) Roland C Wilhelm et al.   ISME Journal

Statistics, Scoring Functions, and Regional Analysis of a Comprehensive Soil Health Database

(2017) Aubrey K. Fine et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

(2017) Florine Degrune et al.   Frontiers in Microbiology

Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity

(2017) Hao-Xun Chang et al.   Frontiers in Microbiology

Soil biota contributions to soil aggregation

(2017) Anika Lehmann et al.   Nature Ecology & Evolution

Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities

(2017) Manuel Delgado-Baquerizo et al.   Nature Ecology & Evolution

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Microbial and biochemical basis of a Fusarium wilt-suppressive soil

(2015) Jae-Yul Cha et al.   ISME Journal

Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22T

(2015) Kevin C. Y. Lee et al.   Standards in Genomic Sciences

The Community Structures of Prokaryotes and Fungi in Mountain Pasture Soils are Highly Correlated and Primarily Influenced by pH

(2015) Anders Lanzén et al.   Frontiers in Microbiology

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

(2015) Elizaveta Pershina et al.   PLoS One

Effect of preservation method on the assessment of bacterial community structure in soil and water samples

(2014) Valeria Tatangelo et al.   FEMS MICROBIOLOGY LETTERS

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison

(2013) Alexander Statnikov et al.   Scientific Reports

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

(2013) Kateryna Zhalnina et al.   Frontiers in Microbiology

Effects of biological soil crusts on surface roughness and implications for runoff and erosion

(2012) Emilio Rodríguez-Caballero et al.   GEOMORPHOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Human-Associated Microbial Signatures: Examining Their Predictive Value

(2011) Dan Knights et al.   Cell Host & Microbe

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

(2011) Ella Wessén et al.   ISME Journal

Bacterial community structures are unique and resilient in full-scale bioenergy systems

(2011) J. J. Werner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

(2010) Christian L. Lauber et al.   FEMS MICROBIOLOGY LETTERS

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Harvested perennial grasslands provide ecological benchmarks for agricultural sustainability

(2009) Jerry D. Glover et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity

(2008) Vesela A. Tzeneva et al.   RESEARCH IN MICROBIOLOGY

Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment

(2008) Ian M. Clark et al.   SOIL BIOLOGY & BIOCHEMISTRY