The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.
Distinguishing random environmental fluctuations from ecological catastrophes for the North Pacific Ocean
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
Methods for detecting early warnings of critical transitions in time series illustrated using simulated ecological data
Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists
Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men
Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression
Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved
Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton
A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets
Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota
Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions
The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome
Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels
Spatiotemporally Heterogeneous Population Dynamics of Gut Bacteria Inferred from Fecal Time Series Data
Extended local similarity analysis (eLSA) reveals unique associations between bacterial community structure and odor emission during pig carcasses decomposition
Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability
Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system
A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia
The relative abundance of alkane-degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil-well products
Hidden drivers of low-dose pharmaceutical pollutant mixtures revealed by the novel GSA-QHTS screening method
Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis
A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series
Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietary shift and ciprofloxacin treatment
Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis
Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling
'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.
Growth Stage-dependent Bacterial Communities in Soybean Plant Tissues: Methylorubrum Transiently Dominated in the Flowering Stage of the Soybean Shoot
Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study
Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data
Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies
Trios-promising in silico biomarkers for differentiating the effect of disease on the human microbiome network
Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China
A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types
Constructing the Microbial Association Network from Large-Scale Time Series Data Using Granger Causality
Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations.
Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification
Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities
Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling.
Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland
Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?
Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis
Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities
Detection of stable community structures within gut microbiota co-occurrence networks from different human populations
Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria
Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale
Physicochemical Factors Affecting Microbiota Dynamics During Traditional Solid-State Fermentation of Chinese Strong-Flavor Baijiu
Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting
Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis
Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back
Coffee consumption revealed sex differences in host endogenous metabolism and gut microbiota in healthy adults.
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment.
Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir.
Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network.
Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions.
Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Alzheimer's Disease: MS4A
Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.
Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.
Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.
Genetic Screens in iPSC-derived Brain Cells
Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.
This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Pharmacology of Proteinopathies
This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.
Alignment-free Sequence Analysis Tools
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