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Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.

Frontiers in microbiology

Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF.
PMID: 26191049
Front Microbiol. 2015 Jul 01;6:654. doi: 10.3389/fmicb.2015.00654. eCollection 2015.

While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do...

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Brooks B, Mueller RS, Young JC, et al. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol. 2015;6:654doi: 10.3389/fmicb.2015.00654.
Brooks, B., Mueller, R. S., Young, J. C., Morowitz, M. J., Hettich, R. L., & Banfield, J. F. (2015). Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Frontiers in microbiology, 6654. https://doi.org/10.3389/fmicb.2015.00654
Brooks, Brandon, et al. "Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant." Frontiers in microbiology vol. 6 (2015): 654. doi: https://doi.org/10.3389/fmicb.2015.00654
Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol. 2015 Jul 01;6:654. doi: 10.3389/fmicb.2015.00654. eCollection 2015. PMID: 26191049; PMCID: PMC4487087.
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Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life.

Microbiome

Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF.
PMID: 24451181
Microbiome. 2013 Dec 17;1(1):30. doi: 10.1186/2049-2618-1-30.

BACKGROUND: The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the...

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Brown CT, Sharon I, Thomas BC, et al. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome. 2013;1(1):30doi: 10.1186/2049-2618-1-30.
Brown, C. T., Sharon, I., Thomas, B. C., Castelle, C. J., Morowitz, M. J., & Banfield, J. F. (2013). Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome, 1(1), 30. https://doi.org/10.1186/2049-2618-1-30
Brown, Christopher T, et al. "Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life." Microbiome vol. 1,1 (2013): 30. doi: https://doi.org/10.1186/2049-2618-1-30
Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome. 2013 Dec 17;1(1):30. doi: 10.1186/2049-2618-1-30. PMID: 24451181; PMCID: PMC4177395.
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Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity.

Genome research

Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF.
PMID: 33361114
Genome Res. 2020 Dec 23; doi: 10.1101/gr.268169.120. Epub 2020 Dec 23.

Biosynthetic gene clusters (BGCs) are operonic sets of microbial genes that synthesize specialized metabolites with diverse functions, including siderophores and antibiotics, which often require export to the extracellular environment. For this reason, genes for transport across cellular membranes are...

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Crits-Christoph A, Bhattacharya N, Olm MR, et al. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res. 2020;doi: 10.1101/gr.268169.120.
Crits-Christoph, A., Bhattacharya, N., Olm, M. R., Song, Y. S., & Banfield, J. F. (2020). Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome research, . https://doi.org/10.1101/gr.268169.120
Crits-Christoph, Alexander, et al. "Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity." Genome research vol. (2020). doi: https://doi.org/10.1101/gr.268169.120
Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res. 2020 Dec 23; doi: 10.1101/gr.268169.120. Epub 2020 Dec 23. PMID: 33361114; PMCID: PMC7849407.
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Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome.

mSystems

Rahman SF, Olm MR, Morowitz MJ, Banfield JF.
PMID: 29359195
mSystems. 2018 Jan 09;3(1). doi: 10.1128/mSystems.00123-17. eCollection 2018.

Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut...

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Rahman SF, Olm MR, Morowitz MJ, et al. Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. mSystems. 2018;3(1)doi: 10.1128/mSystems.00123-17.
Rahman, S. F., Olm, M. R., Morowitz, M. J., & Banfield, J. F. (2018). Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. mSystems, 3(1), . https://doi.org/10.1128/mSystems.00123-17
Rahman, Sumayah F, et al. "Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome." mSystems vol. 3,1 (2018). doi: https://doi.org/10.1128/mSystems.00123-17
Rahman SF, Olm MR, Morowitz MJ, Banfield JF. Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. mSystems. 2018 Jan 09;3(1). doi: 10.1128/mSystems.00123-17. eCollection 2018. PMID: 29359195; PMCID: PMC5758725.
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Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries.

mSystems

Olm MR, Crits-Christoph A, Diamond S, Lavy A, Matheus Carnevali PB, Banfield JF.
PMID: 31937678
mSystems. 2020 Jan 14;5(1). doi: 10.1128/mSystems.00731-19.

Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases,...

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Olm MR, Crits-Christoph A, Diamond S, et al. Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems. 2020;5(1)doi: 10.1128/mSystems.00731-19.
Olm, M. R., Crits-Christoph, A., Diamond, S., Lavy, A., Matheus Carnevali, P. B., & Banfield, J. F. (2020). Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems, 5(1), . https://doi.org/10.1128/mSystems.00731-19
Olm, Matthew R, et al. "Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries." mSystems vol. 5,1 (2020). doi: https://doi.org/10.1128/mSystems.00731-19
Olm MR, Crits-Christoph A, Diamond S, Lavy A, Matheus Carnevali PB, Banfield JF. Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems. 2020 Jan 14;5(1). doi: 10.1128/mSystems.00731-19. PMID: 31937678; PMCID: PMC6967389.
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Showing 1 to 5 of 5 entries