Jillian BANFIELD
University of California, Berkeley
H-index: 149
North America-United States
Description
Jillian BANFIELD, With an exceptional h-index of 149 and a recent h-index of 91 (since 2020), a distinguished researcher at University of California, Berkeley, specializes in the field of Nanogeoscience, Microbial Ecology, Geomicrobiology, Metagenomics, Mineralogy.
His recent articles reflect a diverse array of research interests and contributions to the field:
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism
Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes
Crispr-cas effector polypeptides and methods of use thereof
Vitamin B12 variants structure soil microbial communities despite soil’s vast reservoir of B12
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
Infant gut DNA bacteriophage strain persistence during the first 3 years of life
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
Candidate Phyla Radiation bacteria
Professor Information
University | University of California, Berkeley |
---|---|
Position | ___ |
Citations(all) | 87250 |
Citations(since 2020) | 36266 |
Cited By | 64920 |
hIndex(all) | 149 |
hIndex(since 2020) | 91 |
i10Index(all) | 442 |
i10Index(since 2020) | 375 |
University Profile Page | University of California, Berkeley |
Research & Interests List
Nanogeoscience
Microbial Ecology
Geomicrobiology
Metagenomics
Mineralogy
Top articles of Jillian BANFIELD
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism
BackgroundBiofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.ResultsSulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at …
Authors
Luis E Valentin-Alvarado,Sirine C Fakra,Alexander J Probst,Jonathan R Giska,Alexander L Jaffe,Luke M Oltrogge,Jacob West-Roberts,Joel Rowland,Michael Manga,David F Savage,Chris Greening,Brett J Baker,Jillian F Banfield
Journal
Microbiome
Published Date
2024/1/26
Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes
BackgroundPrior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood.ResultsAlthough there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in …
Authors
Marcos Y Voutsinos,Jacob A West-Roberts,Rohan Sachdeva,John W Moreau,Jillian F Banfield
Journal
BMC biology
Published Date
2024/2/19
Crispr-cas effector polypeptides and methods of use thereof
2023-08-23 Assigned to THE REGENTS OF THE UNIVERSITY OF CALIFORNIA reassignment THE REGENTS OF THE UNIVERSITY OF CALIFORNIA ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: DE LA MORENA, Evangelina Nogales, LIU, Jun-jie, DOUDNA, JENNIFER A., TSUCHIDA, Connor Andrew
Published Date
2023/12/21
Vitamin B12 variants structure soil microbial communities despite soil’s vast reservoir of B12
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids show distinct shifts in bacterial 16S composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
Authors
Zachary F Hallberg,Alexa M Nicolas,Zoila I Alvarez-Aponte,Kenny C Mok,Ella T Sieradzki,Jennifer Pett-Ridge,Jillian F Banfield,Hans K Carlson,Mary K Firestone,Michiko E Taga
Journal
bioRxiv
Published Date
2024/2/12
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of …
Authors
LinXing Chen,Jillian F Banfield
Journal
Nature Microbiology
Published Date
2024/2/6
Infant gut DNA bacteriophage strain persistence during the first 3 years of life
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop …
Authors
Yue Clare Lou,LinXing Chen,Adair L Borges,Jacob West-Roberts,Brian A Firek,Michael J Morowitz,Jillian F Banfield
Journal
Cell Host & Microbe
Published Date
2024/1/10
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their …
Authors
Benjamin A Adler,Marena I Trinidad,Daniel Bellieny-Rabelo,Elaine Zhang,Hannah M Karp,Petr Skopintsev,Brittney W Thornton,Rachel F Weissman,Peter H Yoon,LinXing Chen,Tomas Hessler,Amy R Eggers,David Colognori,Ron Boger,Erin E Doherty,Connor A Tsuchida,Ryan V Tran,Laura Hofman,Honglue Shi,Kevin M Wasko,Zehan Zhou,Chenglong Xia,Muntathar J Al-Shimary,Jaymin R Patel,Vienna CJX Thomas,Rithu Pattali,Matthew J Kan,Anna Vardapetyan,Alana Yang,Arushi Lahiri,Micaela F Maxwell,Andrew G Murdock,Glenn C Ramit,Hope R Henderson,Roland W Calvert,Rebecca S Bamert,Gavin J Knott,Audrone Lapinaite,Patrick Pausch,Joshua C Cofsky,Erik J Sontheimer,Blake Wiedenheft,Peter C Fineran,Stan JJ Brouns,Dipali G Sashital,Brian C Thomas,Christopher T Brown,Daniela SA Goltsman,Rodolphe Barrangou,Virginius Siksnys,Jillian F Banfield,David F Savage,Jennifer A Doudna
Journal
Nucleic acids research
Published Date
2024/1/5
Candidate Phyla Radiation bacteria
What are the ‘Candidate Phyla Radiation’bacteria, and where are they found? Early marker-gene surveys of the microbial world uncovered the presence of a variety of divergent groups of bacteria that had not been cultured in the laboratory. Later, through extensive genomic sampling and phylogenetic analysis, a large group of these ‘candidate phyla’—including those initially known as OP11, SR1, OD1, BD1-5, and PER—were recognized to have evolved from a common ancestor apart from other bacteria, and thus were collectively termed the ‘Candidate Phyla Radiation’(CPR)(Figure 1A). Examination of CPR bacteria via metagenomic techniques that can recover entire genomes established their small genome sizes and limited metabolic potential. Such genetic features fueled speculation that these organisms are likely dependent upon other members of microbial communities for key molecular building blocks …
Authors
Alexander L Jaffe,Jillian F Banfield
Journal
Current Biology
Published Date
2024/2/5
Professor FAQs
What is Jillian BANFIELD's h-index at University of California, Berkeley?
The h-index of Jillian BANFIELD has been 91 since 2020 and 149 in total.
What are Jillian BANFIELD's top articles?
The articles with the titles of
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism
Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes
Crispr-cas effector polypeptides and methods of use thereof
Vitamin B12 variants structure soil microbial communities despite soil’s vast reservoir of B12
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
Infant gut DNA bacteriophage strain persistence during the first 3 years of life
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
Candidate Phyla Radiation bacteria
...
are the top articles of Jillian BANFIELD at University of California, Berkeley.
What are Jillian BANFIELD's research interests?
The research interests of Jillian BANFIELD are: Nanogeoscience, Microbial Ecology, Geomicrobiology, Metagenomics, Mineralogy
What is Jillian BANFIELD's total number of citations?
Jillian BANFIELD has 87,250 citations in total.
What are the co-authors of Jillian BANFIELD?
The co-authors of Jillian BANFIELD are Robert J. Hamers, Gene W. Tyson, Eric E. Allen, Kelly C. Wrighton, Michael Wilkins, Alexander J. Probst.