Evidence map›Paper›PMID 33410932›Full record

ArticleMicrobial ecology2021

Merging Fungal and Bacterial Community Profiles via an Internal Control.

Miriam I Hutchinson, Tisza A S Bell, La Verne Gallegos-Graves, John Dunbar, Michaeline Albright

Open access · greenAbstract read
PubMed Publisher
In one paragraph

Article in Microbial ecology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
1.1field-weighted citation impact, top 19% of its field
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

4 citing papers in PubMed, 7 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 1 institution in 1 country.

Miriam I HutchinsonBiosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.ORCID https://orcid.org/0000-0003-4077-0184
Tisza A S BellBiosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.ORCID https://orcid.org/0000-0002-2773-400X
La Verne Gallegos-GravesBiosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.
John DunbarBiosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.ORCID https://orcid.org/0000-0001-5601-2420
Michaeline AlbrightBiosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA. malbright@lanl.gov.ORCID https://orcid.org/0000-0002-4528-0312
Los Alamos National Laboratory · US

Funding

Office of Science F255LANL2018
6 · The paper itself

Abstract

Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.

Indexed as

FungiMicrobiotaBacteriaDNA, FungalHigh-Throughput Nucleotide SequencingDNA, FungalBacteriaCommunity ecologyFungal-bacterial ratioFungiTargeted metagenomicsTaxonomic profiles

Identifiers

PMID33410932
OpenAlexW3118693270

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.