Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Scientific Reports
Thomas GurryEric J Alm

Abstract

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host's microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient's microbiota.

References

Nov 1, 1995·Biochemical Society Transactions·A P CorfieldC Paraskeva
Oct 22, 1998·Acta Anatomica·I BrockhausenW Kuhns
Feb 16, 2000·The British Journal of Nutrition·H P KruseM Blaut
Jul 25, 2000·Postgraduate Medical Journal·T ShiraziC S Probert
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Nov 8, 2002·British Medical Bulletin·Peter Boyle, Maria Elena Leon
May 31, 2003·Journal of Biology·Roy Kishony, Stanislas Leibler
Mar 26, 2005·Science·Fredrik BäckhedJeffrey I Gordon
Oct 6, 2005·Applied and Environmental Microbiology·Maddalena RossiDiego Matteuzzi
Dec 8, 2005·Applied and Environmental Microbiology·Catherine Lozupone, Rob Knight
Jun 21, 2007·PLoS Biology·Jian XuJeffrey I Gordon
Oct 15, 2008·Genome Biology·Martin Wu, Jonathan A Eisen
Oct 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Harry SokolPhilippe Langella
Apr 21, 2009·Molecular Biology and Evolution·Morgan N PriceAdam P Arkin
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Feb 9, 2010·Journal of Gastroenterology and Hepatology·Peter R Gibson, Susan J Shepherd
May 5, 2010·Nucleic Acids Research·Mickael GoujonRodrigo Lopez
Jul 29, 2010·FEMS Microbiology Ecology·Christophe ChassardAnnick Bernalier-Donadille
Aug 4, 2010·Proceedings of the National Academy of Sciences of the United States of America·Carlotta De FilippoPaolo Lionetti
Aug 17, 2010·Bioinformatics·Robert C Edgar
Dec 21, 2010·Nature Immunology·Kendle M Maslowski, Charles R Mackay
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
Sep 2, 2011·Genome Research·Samuel MinotFrederic D Bushman
May 31, 2012·Nucleic Acids Research·Yanbin YinYing Xu
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Oct 22, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
Dec 18, 2013·Nature·Lawrence A DavidPeter J Turnbaugh
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Aug 26, 2014·Genome Biology·Lawrence A DavidEric J Alm
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Apr 29, 2015·Nature Communications·Stephen J D O'KeefeErwin G Zoetendal
Nov 29, 2015·Nucleic Acids Research·UNKNOWN NCBI Resource Coordinators
Jan 13, 2016·BMC Biology·Wing Sun Faith ChungHarry J Flint
Feb 8, 2016·Trends in Molecular Medicine·Noortje IjssennaggerSaskia W C van Mil

❮ Previous
Next ❯

Citations

Mar 13, 2019·Nature Reviews. Immunology·Ashwin N SkellyKenya Honda
May 3, 2019·Scientific Reports·Rebecca L MaherRebecca Vega Thurber
Jun 16, 2019·Applied and Environmental Microbiology·Car Reen KokRobert Hutkins
Jun 6, 2019·Genome Biology·Keegan KorthauerStephanie C Hicks
Oct 23, 2019·Signal Transduction and Targeted Therapy·Ziying ZhangYongguang Tao
Apr 15, 2020·Nature Microbiology·Brian W JiDennis Vitkup
Nov 27, 2019·Nutrients·Emily R LeemingCaroline I Le Roy
Jul 1, 2020·Frontiers in Nutrition·Abigail J JohnsonAngela M Zivkovic
May 16, 2020·Frontiers in Public Health·Nita Jain
Oct 11, 2020·Signal Transduction and Targeted Therapy·Ziying ZhangYongguang Tao
Jul 21, 2020·Journal of Pharmaceutical and Biomedical Analysis·Thomas Gurry, Leonardo Scapozza
Jun 29, 2021·Microbiome·Alexander S F BerryDaniel P Beiting

❮ Previous
Next ❯

Methods Mentioned

BETA
environmental stresses
amplicon sequencing
Illumina sequencing
PCR

Clinical Trials Mentioned

ISRCTN53935058

Software Mentioned

FastTree
iTOL
DESeq2
BLAST
BWA
PRINSEQ
scikit
bio Python package
EMBOSS Transeq
dbCAN

Related Concepts

Trending Feeds

COVID-19

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.