Evidence map›Paper›PMID 39005317›Full record

ArticlebioRxiv : the preprint server for biology2025

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.

Aleksandr A Arzamasov, Dmitry A Rodionov, Matthew C Hibberd, Janaki L Guruge, James E Kent, Marat D Kazanov, Semen A Leyn, Marinela L Elane, Kristija Sejane, Annalee Furst and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Aleksandr A ArzamasovCenter for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA.ORCID 0000-0002-4150-4817
Dmitry A RodionovCenter for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Matthew C HibberdEdison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Janaki L GurugeEdison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
James E KentCenter for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Marat D KazanovFaculty of Engineering and Natural Sciences, Sabanci University, Istanbul, 34956, Turkey.
Semen A LeynCenter for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Marinela L ElaneCenter for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Kristija SejaneDepartment of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA.
Annalee FurstDepartment of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA.
Lars BodeDepartment of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA.
Michael J BarrattEdison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Jeffrey I GordonEdison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Andrei L OstermanCenter for Data Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA.ORCID 0000-0002-3810-9824

Funding

Tumor Microenvironment and Cancer ImmunologyP30CA030199 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI ELENA B PASQUALE · 1985 to 2026
$107.2M
REGULATION OF GENE EXPRESSION - SMALL INTESTINER01DK030292 · NIDDK · WASHINGTON UNIVERSITY · PI JEFFREY I GORDON, ANDREI L OSTERMAN · 1986 to 2026
$6.5M
REGULATION OF GENE EXPRESSION IN THE SMALL INTESTINER37DK030292 · NIDDK · WASHINGTON UNIVERSITY · PI GORDON, JEFFREY I · 1993 to 2015
$4.0M
Gates Foundation INV-016367NCI NIH HHS P30 CA030199NIDDK NIH HHS R01 DK030292NIDDK NIH HHS R37 DK030292
6 · The paper itself

Abstract

Bifidobacteria are among the earliest colonizers of the human gut and are widely used as probiotics for their health-promoting properties. However, individual responses to probiotic supplementation may vary with strain type(s), microbiota composition, diet, or lifestyle conditions, highlighting the need for strain-level insights into the bifidobacterial metabolism of dietary and host glycans. Here, we systematically reconstructed 68 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the distribution of 589 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 3083 non-redundant cultured

Identifiers

PMID39005317
PMCPMC11245093

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.