Explanipedia

Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i> Open

Allison K. Guitor, Shuai Wang, Owen T. Tuck, Brian Firek, Nadezda Kryuchkova-Mostacci , et al. · 2025

Summary Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in lengt…

CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments Open

Valerie Seitz, Bridget B. McGivern, Michael Shaffer, Mikayla Borton, Aeriel D. Belk , et al. · 2025

Microbial degradation of organic matter is a fundamental Earth process, yet a mechanistic understanding of microbial metabolisms and successional ecology involved in decomposition remains poorly understood. Here, we announce the recovery o…

The human milk microbiome varies by environmental factors and is associated with infant growth: findings from the IMiC Consortium Open

Melissa B. Manus, Kelsey Fehr, Chi-Hung Shu, Andrew Mertens, Mark D. DeBoer , et al. · 2025

Human milk (HM) is a complex ecological matrix that connects mothers and infants to the surrounding environment, and promotes infant growth and health. While certain components of HM are well studied, including its macronutrient content an…

Protocol: the International Milk Composition (IMiC) Consortium - a harmonized secondary analysis of human milk from four studies Open

Kelsey Fehr, Andrew Mertens, Chi-Hung Shu, Trenton Dailey-Chwalibóg, Liat Shenhav , et al. · 2025

Introduction Human milk (HM) contains a multitude of nutritive and nonnutritive bioactive compounds that support infant growth, immunity and development, yet its complex composition remains poorly understood. Integrating diverse scientific…

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies Open

Pixu Shi, Cameron Martino, Rungang Han, Stefan Janssen, Gregory A. Buck , et al. · 2024

A Modified Mediterranean Ketogenic Diet reverses signatures and mitigates modifiable risk factors of Alzheimer’s disease Open

Annalise Schweickart, Kevin Huynh, Richa Batra, Bryan J. Neth, Cameron Martino , et al. · 2024

Background Alzheimer’s disease (AD) is a neurodegenerative disorder with significant environmental factors, including diet, that influence its onset and progression. While the ketogenic diet (KD) holds promise in reducing metabolic risks a…

Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease Open

Annalise Schweickart, Richa Batra, Bryan J. Neth, Cameron Martino, Liat Shenhav , et al. · 2024

Alzheimer’s disease (AD) is influenced by a variety of modifiable risk factors, including a person’s dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a f…

Personalized mood prediction from patterns of behavior collected with smartphones Open

Brunilda Balliu, Chris Douglas, Darsol Seok, Liat Shenhav, Yue Wu , et al. · 2024

Over the last ten years, there has been considerable progress in using digital behavioral phenotypes, captured passively and continuously from smartphones and wearable devices, to infer depressive mood. However, most digital phenotype stud…

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables Open

Zachary M. Burcham, Aeriel D. Belk, Bridget B. McGivern, Amina Bouslimani, Parsa Ghadermazi , et al. · 2024

A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer’s Disease: a serum and CSF-based metabolic analysis Open

Annalise Schweickart, Richa Batra, Bryan J. Neth, Cameron Martino, Liat Shenhav , et al. · 2023

Alzheimer’s disease (AD) is influenced by a variety of modifiable risk factors, including a person’s dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a f…

Microdiversity of the vaginal microbiome is associated with preterm birth Open

Jingqiu Liao, Liat Shenhav, J Urban, Myrna G. Serrano, Bin Zhu , et al. · 2023

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies Open

Pixu Shi, Cameron Martino, Rungang Han, Stefan Janssen, Gregory A. Buck , et al. · 2023

Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudina…

Processed data for Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. Open

Jingqiu Liao, Liat Shenhav, Tal Korem · 2023

Processed data for the manuscript Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth.

Processed data for Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. Open

Jingqiu Liao, Liat Shenhav, Tal Korem · 2023

Processed data for the manuscript Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth.

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data Open

George I. Austin, Heekuk Park, Yoli Meydan, Dwayne Seeram, Tanya Sezin , et al. · 2023

Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth Open

Jingqiu Liao, Liat Shenhav, J Urban, Myrna G. Serrano, Bin Zhu , et al. · 2023

Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic ada…

Personalized Mood Prediction from Patterns of Behavior Collected with Smartphones Open

Brunilda Balliu, Chris Douglas, Darsol Seok, Liat Shenhav, Yue Wu , et al. · 2022

Over the last ten years, there has been considerable progress in using digital behavioral phenotypes, captured passively and continuously from smartphones and wearable devices, to infer depressive mood. However, most digital phenotype stud…

STENSL: Microbial Source Tracking with ENvironment SeLection Open

Ulzee An, Liat Shenhav, C. Anders Olson, Elaine Y. Hsiao, Eran Halperin , et al. · 2022

Microbial source tracking is a powerful tool to characterize the properties of complex microbial communities. However, this analysis is currently limited to source environments sampled in a specific study.

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype Open

Cameron Martino, Daniel McDonald, Kalen Cantrell, Amanda Hazel Dilmore, Yoshiki Vázquez‐Baeza , et al. · 2022

Microbiome data analysis can be difficult because of particular data features, some unavoidable and some due to technical limitations of DNA sequencing instruments. The first step in many analyses that ultimately reveals patterns of simila…

Quantifying Replicability and Consistency in Systematic Reviews Open

Iman Jaljuli, Yoav Benjamini, Liat Shenhav, Orestis A. Panagiotou, Ruth Heller · 2022

Systematic reviews and meta-analyses are important tools for synthesizing evidence from multiple studies. They serve to increase power and improve precision, in the same way that large studies can do, but also to establish the consistency …

Using Community Ecology Theory and Computational Microbiome Methods To Study Human Milk as a Biological System Open

Liat Shenhav, Meghan B. Azad · 2022

Human milk is a complex and dynamic biological system that has evolved to optimally nourish and protect human infants. Yet, according to a recent priority-setting review, “our current understanding of human milk composition and its individ…

Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding Open

Se Jin Song, Jincheng Wang, Cameron Martino, Lingjing Jiang, Wesley K. Thompson , et al. · 2021

The Discriminatory Power of Vocal Features in Detecting Mental Illnesses Under Complex Context Open

Wei Pan, Liat Shenhav, Amber Afshan, Abeer Alwan, Jonathan Flint , et al. · 2021

Background: Vocal features have been proposed as a way to identify depression by distinguishing depression from healthy controls, but while there have been some claims for success, the degree to which changes in vocal features are specific…

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics Open

Cameron Martino, Liat Shenhav, Clarisse Marotz, George Armstrong, Daniel McDonald , et al. · 2020

Resource conservation manifests in the genetic code Open

Liat Shenhav, David Zeevi · 2020

Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this ‘resource-driven’ select…

Compositional Lotka-Volterra describes microbial dynamics in the simplex Open

Tyler Joseph, Liat Shenhav, João B. Xavier, Eran Halperin, Itsik Pe’er · 2020

Dynamic changes in microbial communities play an important role in human health and disease. Specifically, deciphering how microbial species in a community interact with each other and their environment can elucidate mechanisms of disease,…

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics Open

Ori Furman, Liat Shenhav, Goor Sasson, Fotini Kokou, Hen Honig , et al. · 2020

Resource conservation manifests in the genetic code Open

Liat Shenhav, David Zeevi · 2019

Nutrient limitation is a strong selective force, driving competition for resources. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this ‘resource-d…

Quantifying replicability and consistency in systematic reviews Open

Iman Jaljuli, Yoav Benjamini, Liat Shenhav, Orestis A. Panagiotou, Ruth Heller · 2019

Systematic reviews of interventions are important tools for synthesizing evidence from multiple studies. They serve to increase power and improve precision, in the same way that larger studies can do, but also to establish the consistency …

Modeling the temporal dynamics of the gut microbial community in adults and infants Open

Liat Shenhav, Ori Furman, Leah Briscoe, Michael Thompson, Justin D. Silverman , et al. · 2019

Given the highly dynamic and complex nature of the human gut microbial community, the ability to identify and predict time-dependent compositional patterns of microbes is crucial to our understanding of the structure and functions of this …

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