A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.
Paper
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The authors' code
Shell · 20 lines · 495 B · no license
- #!/bin/sh
- # use this script to run copies per million normalization (i.e. for maaslin2 input) on
- ## humann output
- # apply loop to files (gene families, path abundance, path coverage for each sample) in humann output dir
- for FILE in ../w1_humann_output/*.tsv;
- do
- if [[ $FILE != *"coverage"* ]]; then
- echo "running " "$FILE";
- # normalize to relative abundance (reads per million; '%%.*' removes extension)
- humann_renorm_table -i $FILE -o ${FILE/.tsv/}_copiespermillion.tsv -u cpm
- fi
- done
humann_normalize_loop.sh at commit dc770e8, no license · at the source
Overview
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Lanser Westman Psychology Group, Los Angeles, CA, 90025, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience at University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases at University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Goodman-Luskin Microbiome Center at University of California, Los Angeles, Los Angeles, CA, 90095, USA
- David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, 90075, USA
Abstract
Caregiving-related early adversities (crEAs) are potent risk factors for the development of internalizing psychopathology (e.g., depression, anxiety). Alterations to the dopaminergic mesocorticolimbic system, which supports the construction of reward-related experiences, are commonly observed following crEA exposure and are thought to mediate this risk. Indeed, many internalizing disorders are characterized by disruptions in how reward-related information is represented and used to guide affective and motivational states. Critically, the effects of crEA on mesocorticolimbic functioning may be shaped by input from peripheral systems, such as the gut microbiome, though such bottom-up signaling has been markedly understudied in humans. The Teen Bugs study was thus developed to identify gut microbiome-dependent metabolic pathways linking crEA exposure to mesocorticolimbic functioning and internalizing symptoms in adolescents, a group that experiences a disproportionate incidence of psychopathology relative to other age groups and is underrepresented in the gut microbiome literature. Adolescents aged 12–15 years, with and without histories of crEA exposure, will be followed across three timepoints over five years. At each timepoint, participants will complete a semi-structured clinical interview, a reward-guided decision-making task, and self-report questionnaires assessing mental health, previous caregiving experiences, reward-related behaviors, as well as developmental and lifestyle factors. Participants will also undergo multimodal neuroimaging that leverages MRI-based proxy markers of dopaminergic neurobiology and provide stool and blood samples for metagenomic and metabolomic profiling, respectively. This integrative design has the potential to clarify developmentally salient mechanisms that may serve as novel therapeutic targets for youth most at risk of, or already experiencing, internalizing psychopathology.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above.
bablab/bablab_hoffman_metagenomics
dc770e890987b2932cd2a353b8673f64b4db37ef, 29 May 2025Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
7 files
- humann_normalize_loop.sh
, Shell, 20 lines - humann_reduce_pathways.R
, R, 19 lines - run_humann.sh, Shell, 50 lines
- run_kneaddata_forloop.sh
, Shell, 43 lines - run_metaphlan.sh, Shell, 38 lines
- run_metaphlan_merged.sh, Shell, 38 lines
- README.md, Text, 77 lines
Tracing map
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Data
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Data availability
No data was used for the research described in the article.
Reproduced under the paper's license (CC BY), from the paper cited above.
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Version 2, 28 September 2026
- Authors: added Genesis D Flores (0000-0002-6480-5524); removed Genesis D Flores
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 17 authors, 6 keywords, 3 funders, 182 references.
Cite
This paper
Flores, G. D., Damon, Z. F., Ford, M., Gancz, N. N., Savoca, P. W., Esfand, S. M., Chu, K. A., Querdasi, F. R., McCann, C. F., Westman, J. G., Labus, J. S., Clewett, D., Parr, A. C., Hsiao, E. Y., Jacobs, J., Silvers, J., & Callaghan, B. L. (2026). A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving. Brain, behavior, & immunity - health, 55, 101275. https://
BibTeX
@article{flores2026proto
author = {Flores, Genesis D and Damon, Zoe F and Ford, Mary and Gancz, Naomi N and Savoca, Paul W and Esfand, Shiba M and Chu, Kristen A and Querdasi, Francesca R and McCann, Clare F and Westman, Jonathan G and Labus, Jennifer S and Clewett, David and Parr, Ashley C and Hsiao, Elaine Y and Jacobs, Jonathan and Silvers, Jennifer and Callaghan, Bridget L},
title = {{A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving}},
journal = {Brain, behavior, \& immunity - health},
year = {2026},
month = jun,
volume = {55},
pages = {101275},
publisher = {Elsevier},
issn = {2666-3546},
doi = {10.1016/
url = {https://
pmid = {42358480},
pmcid = {PMC13292554}
}
RIS
TY - JOUR
AU - Flores, Genesis D
AU - Damon, Zoe F
AU - Ford, Mary
AU - Gancz, Naomi N
AU - Savoca, Paul W
AU - Esfand, Shiba M
AU - Chu, Kristen A
AU - Querdasi, Francesca R
AU - McCann, Clare F
AU - Westman, Jonathan G
AU - Labus, Jennifer S
AU - Clewett, David
AU - Parr, Ashley C
AU - Hsiao, Elaine Y
AU - Jacobs, Jonathan
AU - Silvers, Jennifer
AU - Callaghan, Bridget L
TI - A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving
T2 - Brain, behavior, & immunity - health
J2 - Brain Behav Immun Health
PY - 2026
DA - 2026/
VL - 55
SP - 101275
SN - 2666-3546
PB - Elsevier
DO - 10.1016/
UR - https://
LA - en
ER -
CSL-JSON
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