Su Z, Gao Y, Dong L, He Y, Guo Q, Ma P
Probiotics Antimicrob Proteins. 2025; .
PMID: 40080094
DOI: 10.1007/s12602-025-10503-8.
Schrader L, Brischke C, Trautner J, Tebbe C
Appl Microbiol Biotechnol. 2025; 109(1):59.
PMID: 40044964
PMC: 11882669.
DOI: 10.1007/s00253-025-13443-z.
Liu X, Yang H, Wang J
PLoS One. 2025; 20(3):e0315864.
PMID: 40043034
PMC: 11882092.
DOI: 10.1371/journal.pone.0315864.
Mouratidis I, Konnaris M, Konnaris M, Chantzi N, Chan C, Patsakis M
Genome Res. 2025; 35(2):279-295.
PMID: 39746719
PMC: 11874967.
DOI: 10.1101/gr.280070.124.
Zou J, Xu B, Gao H, Luo P, Chen T, Duan H
Front Immunol. 2024; 15:1507355.
PMID: 39703512
PMC: 11655508.
DOI: 10.3389/fimmu.2024.1507355.
SPLANG-a synthetic poisson-lognormal-based abundance and network generative model for microbial interaction inference algorithms.
Qian W, Stanley K, Aziz Z, Aziz U, Siciliano S
Sci Rep. 2024; 14(1):25099.
PMID: 39443578
PMC: 11499831.
DOI: 10.1038/s41598-024-76513-8.
MetaCompass: Reference-guided Assembly of Metagenomes.
Luan T, Cepeda V, Liu B, Bowen Z, Ayyangar U, Almeida M
ArXiv. 2024; .
PMID: 38903742
PMC: 11188144.
Influence of on composition and function of gastric microbiota in patients with chronic non-atrophic gastritis.
Zhao F, Yan L, Wang P, Zhang K, Hu S
Heliyon. 2024; 10(10):e31472.
PMID: 38818182
PMC: 11137540.
DOI: 10.1016/j.heliyon.2024.e31472.
A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes.
Pastusiak A, Reddy M, Chen X, Hoyer I, Dorman J, Gebhardt M
Commun Biol. 2024; 7(1):667.
PMID: 38816486
PMC: 11139907.
DOI: 10.1038/s42003-024-06337-9.
Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems.
Song Y, Yao S, Li X, Wang T, Jiang X, Bolan N
Eco Environ Health. 2024; 3(2):227-237.
PMID: 38680731
PMC: 11047296.
DOI: 10.1016/j.eehl.2024.03.001.
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
Song L, Langmead B
Genome Biol. 2024; 25(1):106.
PMID: 38664753
PMC: 11046777.
DOI: 10.1186/s13059-024-03244-4.
Ten common issues with reference sequence databases and how to mitigate them.
Chorlton S
Front Bioinform. 2024; 4:1278228.
PMID: 38560517
PMC: 10978663.
DOI: 10.3389/fbinf.2024.1278228.
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences.
Hauswedell H, Hetzel S, Gottlieb S, Kretzmer H, Meissner A, Reinert K
Bioinformatics. 2024; 40(3).
PMID: 38485699
PMC: 10955267.
DOI: 10.1093/bioinformatics/btae097.
Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China.
Rui Y, Qiu G
Microorganisms. 2024; 12(2).
PMID: 38399800
PMC: 10893252.
DOI: 10.3390/microorganisms12020396.
Emergent Functional Organization of Gut Microbiomes in Health and Diseases.
Seppi M, Pasqualini J, Facchin S, Savarino E, Suweis S
Biomolecules. 2024; 14(1).
PMID: 38275746
PMC: 10813293.
DOI: 10.3390/biom14010005.
Narrative review of application of metagenomic approaches to study the link between oropharyngeal microbiome and infectious diseases.
Diallo K, Missa K, Tuo J, Amoikon T, Bla B, Bonfoh B
Front Microbiol. 2024; 14:1292526.
PMID: 38163063
PMC: 10755466.
DOI: 10.3389/fmicb.2023.1292526.
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
Song L, Langmead B
bioRxiv. 2023; .
PMID: 38014029
PMC: 10680779.
DOI: 10.1101/2023.11.15.567129.
Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.
Zhang Y, Kitazumi A, Liao Y, de Los Reyes B, Wu V
Microbiol Spectr. 2023; 11(5):e0022623.
PMID: 37754684
PMC: 10581182.
DOI: 10.1128/spectrum.00226-23.
Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.
Gu X, Cao Z, Zhao L, Seswita-Zilda D, Zhang Q, Fu L
Int J Mol Sci. 2023; 24(13).
PMID: 37446198
PMC: 10342065.
DOI: 10.3390/ijms241311019.
Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing.
Lee A, Chan C, Wong L, Yip C, Lui W, Cheng K
Front Microbiol. 2023; 14:1164632.
PMID: 37125165
PMC: 10133568.
DOI: 10.3389/fmicb.2023.1164632.