Evidence map›Paper›PMID 40519056›Full record

ArticleG3 (Bethesda, Md.)2025

Genomic and transcriptomic characterization of carbohydrate-active enzymes in the anaerobic fungus Neocallimastix cameroonii var. constans.

Elaina M Blair, Tejas A Navaratna, Colleen B Ahern, Ramya Ragunathan, Jennifer L Brown, Stephen J Mondo, Anna Lipzen, Radwa A Hanafy, Kurt LaButti, Jayson Talag and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Review
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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

17 authors.

Elaina M BlairDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Tejas A NavaratnaDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Colleen B AhernDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0000-0001-9003-4420
Ramya RagunathanDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Jennifer L BrownDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Stephen J MondoU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Anna LipzenU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Radwa A HanafyDepartment of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
Kurt LaButtiU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Jayson TalagArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Kerrie BarryU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Mansi ChovatiaU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Mei WangU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Jessy GonzalezDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Xuefeng PengDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Igor V GrigorievU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Michelle A O'MalleyDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0000-0002-6065-8491

Funding

Department of Energy (DOE) Joint BioEnergy InstituteDepartment of Energy, Office of Science DE-SC0020420Department of Energy, Office of Science DE-SC0022142Institute for Collaborative Biotechnologies W911NF-19-2-0026Institute for Collaborative Biotechnologies W911NF-19-D-0001Lawrence Berkeley National LaboratoryNational Science Foundation 2128271National Science Foundation CNS-1725797Office of Biological and Environmental Research of the DOE Office of Science DE-AC02-05CH11231Office of Science of the U.S. Department of Energy DE-AC02-05CH11231
6 · The paper itself

Abstract

Anaerobic gut fungi effectively degrade lignocellulose in the guts of large herbivores, but there remain a limited number of isolated, publicly available, and sequenced strains that impede our understanding of the role of anaerobic fungi within microbial communities. We isolated and characterized a new fungal isolate, Neocallimastix cameroonii var. constans, providing a transcriptomic and genomic understanding of its ability to degrade diverse carbohydrates. This anaerobic fungal strain was stably cultivated for multiple years in vitro among members of an initial enrichment microbial community derived from goat feces, and it demonstrated the ability to pair with other microbial members, namely, archaeal methanogens to produce methane from lignocellulose. Genomic analysis revealed a higher number of predicted carbohydrate-active enzymes encoded in the N. cameroonii var. constans genome compared to most other sequenced anaerobic fungi. The carbohydrate-active enzyme profile for this isolate contained 660 glycoside hydrolases, 160 carbohydrate esterases, 194 glycosyltransferases, and 85 polysaccharide lyases. Differential gene expression analysis showed the upregulation of thousands of genes (including predicted carbohydrate-active enzymes) when N. cameroonii var. constans was grown on lignocellulose (reed canary grass) compared to less complex substrates, such as cellulose (filter paper), cellobiose, and glucose. AlphaFold was used to predict functions of transcriptionally active yet poorly annotated genes, revealing feruloyl esterases that likely play an important role in lignocellulose degradation by anaerobic fungi. The combination of this strain's genomic and transcriptomic characterization, omics-informed structural prediction, and robustness in microbial co-culture make it a well-suited platform to conduct future investigations into bioprocessing and enzyme discovery.

Indexed as

Carbohydrate MetabolismFungal ProteinsGenome, FungalGenomicsNeocallimastixTranscriptomeAnaerobiosisAnimalsGene Expression ProfilingLigninPhylogenyFungal ProteinsLigninlignocelluloseanaerobic fungiCAZymesenzymegenome assemblylignocelluloseRNA-seq

Identifiers

PMID40519056
PMCPMC12341934

What OpenQuestion holds

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Registered trials

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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.