Nature Search

Publisher Correction: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome

Miles Richardson
Shijie Zhao
Harris H. Wang
Amendments and Corrections11 Feb 2025
Nature Microbiology

Volume: 10, P: 810
High-throughput microbial culturomics using automation and machine learning

A machine learning isolation and genotyping platform enable high-throughput bacterial culture generation.

Yiming Huang
Ravi U. Sheth
Harris H. Wang
ResearchOpen Access20 Feb 2023
Nature Biotechnology

Volume: 41, P: 1424-1433
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome

Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

Miles Richardson
Shijie Zhao
Harris H. Wang
Research03 Feb 2025
Nature Microbiology

Volume: 10, P: 527-540
Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

Horizontal gene transfer (HGT) in complex bacterial communities has been mostly studied using metagenomic analyses. Here, the authors develop an E. coli CRISPR-Cas spacer acquisition platform that allows real-time recording of HGT events at nucleotide-resolution, identifying diverse DNA transfer events in human clinical fecal samples.

Christian Munck
Ravi U. Sheth
Harris H. Wang
ResearchOpen Access07 Jan 2020
Nature Communications

Volume: 11, P: 1-11
Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

DIVERS uses replicate sampling and spike-in sequencing to distinguish temporal and spatial variations from noise in microbial samples.

Brian W. Ji
Ravi U. Sheth
Dennis Vitkup
Research15 Jul 2019
Nature Methods

Volume: 16, P: 731-736
Macroecological dynamics of gut microbiota

Using macroecological approaches and human and murine gut microbiota datasets, the authors demonstrate that the dynamics of these complex microbial communities can be characterized similarly to other ecological systems by multiple quantitative relationships. The observed macroecological relationships were then used to identify specific taxa that are impacted by environmental changes.

Brian W. Ji
Ravi U. Sheth
Dennis Vitkup
Research13 Apr 2020
Nature Microbiology

Volume: 5, P: 768-775
Constraining black hole–galaxy scaling relations and radiative efficiency from galaxy clustering

The large-scale spatial distribution of local active galactic nuclei can constrain the black hole–stellar mass relation and their mean radiative efficiency to 10–20%, suggesting moderate to high spins for the vast majority of supermassive black holes.

Francesco Shankar
Viola Allevato
Ravi K. Sheth
Research09 Dec 2019
Nature Astronomy

Volume: 4, P: 282-291
Robust direct digital-to-biological data storage in living cells

A new DNA data storage technology—data recording in vivo by electrical stimulation (DRIVES)—places CRISPR-based DNA encoding activity under electrochemical control by coupling cellular redox state to CRISPR array gene expression.

Sung Sun Yim
Ross M. McBee
Harris H. Wang
Research11 Jan 2021
Nature Chemical Biology

Volume: 17, P: 246-253
Rewiring bacterial two-component systems by modular DNA-binding domain swapping

Rewiring of bacterial two-component systems (TCSs) was achieved by DNA-binding domain swapping of the two largest response regulator families, which enables cross-species porting and provides a tool for identifying ligands for uncharacterized TCSs.

Sebastian R. Schmidl
Felix Ekness
Jeffrey J. Tabor
Research20 May 2019
Nature Chemical Biology

Volume: 15, P: 690-698
DNA-based memory devices for recording cellular events

In this Review, Sheth and Wang describe emerging synthetic biology approaches for using DNA as a memory device for recording cellular events, including the various methodological steps from detecting diverse signals, converting them into DNA alterations and reading out and interpreting the recorded information. Furthermore, they discuss potential applications as biotechnological and environmental biosensors.

Ravi U. Sheth
Harris H. Wang
Reviews20 Sept 2018
Nature Reviews Genetics

Volume: 19, P: 718-732
A germline-specific class of small RNAs binds mammalian Piwi proteins

One of two studies that identifies a new class of small RNAs that interact with one Argonaute subfamily, the Piwi class. These testis-specific small RNAs, called 'piRNAs', are slightly longer than the previously described siRNAs and miRNAs.

Angélique Girard
Ravi Sachidanandam
Michelle A. Carmell
Research04 Jun 2006
Nature

Volume: 442, P: 199-202
High-throughput transcriptomics of 409 bacteria–drug pairs reveals drivers of gut microbiota perturbation

High-throughput bacterial transcriptomics of 409 drug–microorganism interactions reveals mechanistic insights into drug-mediated microbiota shifts.

Deirdre Ricaurte
Yiming Huang
Harris H. Wang
Research17 Jan 2024
Nature Microbiology

Volume: 9, P: 561-575
Spatial metagenomic characterization of microbial biogeography in the gut

The spatial distribution of bacterial species in the mouse gut is measured by microscopic ‘plot sampling’.

Ravi U. Sheth
Mingqiang Li
Harris H. Wang
Research22 Jul 2019
Nature Biotechnology

Volume: 37, P: 877-883
A framework for human microbiome research

The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.

Barbara A. Methé
Karen E. Nelson
Owen White
ResearchOpen Access13 Jun 2012
Nature

Volume: 486, P: 215-221
Organic ligands and CO₂ unlock the potential for energy relevant metals recovery and carbon mineralization from mafic rocks

Shreya Katre
Prince Ochonma
Greeshma Gadikota
ResearchOpen Access29 Mar 2025
Scientific Reports

Volume: 15, P: 1-21
Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

Curtis Huttenhower
Dirk Gevers
Owen White
ResearchOpen Access13 Jun 2012
Nature

Volume: 486, P: 207-214
Second-generation shRNA libraries covering the mouse and human genomes

Jose M Silva
Mamie Z Li
Gregory J Hannon
Research02 Oct 2005
Nature Genetics

Volume: 37, P: 1281-1288
Microenvironmental CXCL12 deletion enhances Flt3-ITD acute myeloid leukemia stem cell response to therapy by reducing p38 MAPK signaling

Nicholas R. Anderson
Vipul Sheth
Ravi Bhatia
Research22 Dec 2022
Leukemia

Volume: 37, P: 560-570

Search

Publisher Correction: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome

High-throughput microbial culturomics using automation and machine learning

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

Macroecological dynamics of gut microbiota

Constraining black hole–galaxy scaling relations and radiative efficiency from galaxy clustering

Robust direct digital-to-biological data storage in living cells

Rewiring bacterial two-component systems by modular DNA-binding domain swapping

DNA-based memory devices for recording cellular events

A germline-specific class of small RNAs binds mammalian Piwi proteins

High-throughput transcriptomics of 409 bacteria–drug pairs reveals drivers of gut microbiota perturbation

Spatial metagenomic characterization of microbial biogeography in the gut

A framework for human microbiome research

Organic ligands and CO₂ unlock the potential for energy relevant metals recovery and carbon mineralization from mafic rocks

Structure, function and diversity of the healthy human microbiome

Second-generation shRNA libraries covering the mouse and human genomes

Microenvironmental CXCL12 deletion enhances Flt3-ITD acute myeloid leukemia stem cell response to therapy by reducing p38 MAPK signaling

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