Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

Authors: Banfield, Jillian F.^{Aff1, Aff2, Aff3, Aff4, IDs41467025656467_cor1}, Valentin-Alvarado, Luis E.^{Aff1, Aff2, Aff5}, Shi, Ling-Dong, Robinson, Colin Michael, Bamert, Rebecca S., Coulibaly, Fasseli, Barth, Zachary K., Aylward, Frank O., Schoelmerich, Marie C.^{Aff2, Aff7}, Lei, Shufei, Sachdeva, Rohan, Knott, Gavin J.^{Aff1, IDs41467025656467_cor2}

Source: Nature Communications. 16(1)

Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.

Authors: Amano, Yuki, Sachdeva, Rohan, Gittins, Daniel, Anantharaman, Karthik, Lei, Shufei, Valentin-Alvarado, Luis, Diamond, Spencer, Beppu, Hikari, Iwatsuki, Teruki, Mochizuki, Akihito, Miyakawa, Kazuya, Ishii, Eiichi, Murakami, Hiroaki, Jaffe, Alexander, Castelle, Cindy, Lavy, Adi, Suzuki, Yohey, Banfield, Jillian

Source: Standards in Genomic Sciences. 19(1)

Subject Terms: Granite, Groundwater, Metagenomics microbiome, Sedimentary rocks, Stability, Underground research laboratory

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/5pp6v0nf
https://escholarship.org/content/qt5pp6v0nf/qt5pp6v0nf.pdf

Asgard archaea modulate potential methanogenesis substrates in wetland soil.

Authors: Valentin-Alvarado, Luis, Appler, Kathryn, De Anda, Valerie, Schoelmerich, Marie, West-Roberts, Jacob, Kivenson, Veronika, Crits-Christoph, Alexander, Ly, Lynn, Sachdeva, Rohan, Greening, Chris, Savage, David, Baker, Brett, Banfield, Jillian

Source: Nature Communications. 15(1)

Subject Terms: Wetlands, Methane, Soil Microbiology, Archaea, Carbon Cycle, Soil, Phylogeny, Genome, Archaeal, Oxidation-Reduction

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/2vj1b28x
https://escholarship.org/content/qt2vj1b28x/qt2vj1b28x.pdf

Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes.

Authors: Voutsinos, Marcos, West-Roberts, Jacob, Sachdeva, Rohan, Moreau, John, Banfield, Jill

Source: Journal of Biology. 22(1)

Subject Terms: Lanthanides, Metagenomics, Metallophore, Methanol oxidation, Mineralogy, Rare earth elements, Weathered granite, Lanthanoid Series Elements, Methanol, Soil, Bacteria, Phosphates, Minerals, Lanthanum, Silicon Dioxide

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/0114p2bh
https://escholarship.org/content/qt0114p2bh/qt0114p2bh.pdf

Parenting styles, parenting interventions, and childhood obesity

Authors: Sachdeva, Rohan ^a, Sneed, Nadia Markie ^{b, ⁎}

Source: In Current Problems in Pediatric and Adolescent Health Care October 2025 55(10)

A preliminary design of cloud chamber for enhancing interconnections between cosmic rays and humans

Authors: Tanaka, Yuri ^{a, ⁎}, Ariga, Akitaka ^b, Bruckmayr, Chris ^c, Dinulović, Pavle ^d, Kose, Umut ^e, Sachdeva, Rohan ^f

Source: In Acta Astronautica October 2025 235:355-361

Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms

Authors: Hessler, Tomas, Huddy, Robert J, Sachdeva, Rohan, Lei, Shufei, Harrison, Susan TL, Diamond, Spencer, Banfield, Jillian F

Source: Nature Communications. 14(1)

Subject Terms: Microbiology, Biological Sciences, Ecology, Microbiome, Nutrition, Generic health relevance, Metagenomics, Vitamins, Microbiota, Metagenome, Comamonadaceae, Thiamine

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/16k0661t
https://escholarship.org/content/qt16k0661t/qt16k0661t.pdf

Borgs are giant genetic elements with potential to expand metabolic capacity

Authors: Al-Shayeb, Basem, Schoelmerich, Marie C, West-Roberts, Jacob, Valentin-Alvarado, Luis E, Sachdeva, Rohan, Mullen, Susan, Crits-Christoph, Alexander, Wilkins, Michael J, Williams, Kenneth H, Doudna, Jennifer A, Banfield, Jillian F

Source: Nature. 610(7933)

Subject Terms: 31 Biological Sciences (for-2020), 3105 Genetics (for-2020), Genetics (rcdc), Human Genome (rcdc), 1.1 Normal biological development and functioning (hrcs-rac), 13 Climate Action (sdg), Amino Acids (mesh), Anaerobiosis (mesh), Cytochromes (mesh), Ecosystem (mesh), Geologic Sediments (mesh), Greenhouse Gases (mesh), Methane (mesh), Methanosarcinales (mesh), Oxidation-Reduction (mesh), Phylogeny (mesh), Soil (mesh), Methanosarcinales (mesh), Methane (mesh), Cytochromes (mesh), Amino Acids (mesh), Soil (mesh), Ecosystem (mesh), Phylogeny (mesh), Anaerobiosis (mesh), Oxidation-Reduction (mesh), Geologic Sediments (mesh), Greenhouse Gases (mesh), Amino Acids (mesh), Anaerobiosis (mesh), Cytochromes (mesh), Ecosystem (mesh), Geologic Sediments (mesh), Greenhouse Gases (mesh), Methane (mesh), Methanosarcinales (mesh), Oxidation-Reduction (mesh), Phylogeny (mesh), Soil (mesh), General Science & Technology (science-metrix)

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/5675b17c
https://escholarship.org/content/qt5675b17c/qt5675b17c.pdf

Monitoring SARS-CoV-2 incidence and seroconversion among university students and employees: a longitudinal cohort study in California, June–August 2020

Authors: Hunter, Lauren A, Wyman, Stacia, Packel, Laura J, Facente, Shelley N, Li, Yi, Harte, Anna, Nicolette, Guy, Consortium, the IGI SARS-CoV-2 Testing, Di Germanio, Clara, Busch, Michael P, Reingold, Arthur L, Petersen, Maya L, Urnov, Fyodor, McDevitt, Shana, Hirsch, Ariana, Ehrenberg, Alexander, Doudna, Jennifer A, Amen, M, Barry, Kerrie W, Boyle, John M, Brook, Cara E, Choo, Seunga, Cornmesser, Dilworth, David J, Fedrigo, Indro, Friedline, Skyler E, Graham, Thomas GW, Green, Ralph, Hamilton, Jennifer R, Hochstrasser, Megan L, Hockemeyer, Dirk, Krishnappa, Netravathi, Lari, Azra, Li, Hanqin, Lin-Shiao, Enrique, Lu, Tianlin, Lyons, Elijah F, Mark, Kevin G, Martell, Lisa Argento, Martins, A Raquel O, Mitchell, Patrick S, Moehle, Erica A, Naca, Christine, Nandakumar, Divya, O’Brien, Elizabeth, Pappas, Derek J, Pestal, Kathleen, Quach, Diana L, Rubin, Benjamin E, Sachdeva, Rohan, Stahl, Elizabeth C, Syed, Abdullah Muhammad, Tan, I-Li, Tollner, Amy L, Tsuchida, Connor A, Tsui, C Kimberly, Turkalo, Timothy K, Warf, M Bryan, Whitney, Oscar N, Witkowsky, Lea B

Source: BMJ Open. 13(4)

Subject Terms: Biodefense, Emerging Infectious Diseases, Infectious Diseases, Vaccine Related, Prevention, Clinical Research, Infection, Good Health and Well Being, Humans, SARS-CoV-2, COVID-19, Incidence, COVID-19 Testing, Longitudinal Studies, Universities, Seroconversion, Phylogeny, Prospective Studies, California, Cohort Studies, EPIDEMIOLOGY, Public health, Infection control, Epidemiology, PUBLIC HEALTH, IGI SARS-CoV-2 Testing Consortium, Clinical Sciences, Public Health and Health Services, Other Medical and Health Sciences

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/6nm189kx
https://escholarship.org/content/qt6nm189kx/qt6nm189kx.pdf

Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements

Authors: Shi, Ling-Dong, West-Roberts, Jacob, Schoelmerich, Marie C.^{Aff1, Aff5}, Penev, Petar I., Chen, LinXing, Amano, Yuki, Lei, Shufei, Sachdeva, Rohan, Banfield, Jillian F.^{Aff1, Aff2, Aff4, IDs41564024017408_cor9}

Source: Nature Microbiology. 9(9):2422-2433

Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins

Authors: Schoelmerich, Marie Charlotte, Sachdeva, Rohan, West-Roberts, Jacob, Waldburger, Lucas, Banfield, Jillian F

Source: PLOS Biology. 21(1)

Subject Terms: Prevention, Archaea, Tandem Repeat Sequences, Proteins, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/0792c1jg
https://escholarship.org/content/qt0792c1jg/qt0792c1jg.pdf

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Authors: Schoelmerich, Marie C.^{Aff1, Aff12}, Ly, Lynn, West-Roberts, Jacob, Shi, Ling-Dong, Shen, Cong^{Aff4, Aff5}, Malvankar, Nikhil S.^{Aff4, Aff5}, Taib, Najwa, Gribaldo, Simonetta, Woodcroft, Ben J., Schadt, Christopher W.^{Aff8, Aff9}, Al-Shayeb, Basem, Dai, Xiaoguang, Mozsary, Christopher, Hickey, Scott, He, Christine, Beaulaurier, John, Juul, Sissel, Sachdeva, Rohan, Banfield, Jillian F.^{Aff1, Aff3, Aff10, Aff11, IDs41467024495488_cor19}

Source: Nature Communications. 15(1)

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Authors: Borges, Adair L, Lou, Yue Clare, Sachdeva, Rohan, Al-Shayeb, Basem, Penev, Petar I, Jaffe, Alexander L, Lei, Shufei, Santini, Joanne M, Banfield, Jillian F

Source: Nature Microbiology. 7(6)

Subject Terms: Genetics, Aetiology, 2.2 Factors relating to the physical environment, Infection, Animals, Bacteria, Bacteriophages, Biological Evolution, Codon, Terminator, Proteins, Microbiology, Medical Microbiology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/9415j2sq
https://escholarship.org/content/qt9415j2sq/qt9415j2sq.pdf

Species- and site-specific genome editing in complex bacterial communities

Authors: Rubin, Benjamin E, Diamond, Spencer, Cress, Brady F, Crits-Christoph, Alexander, Lou, Yue Clare, Borges, Adair L, Shivram, Haridha, He, Christine, Xu, Michael, Zhou, Zeyi, Smith, Sara J, Rovinsky, Rachel, Smock, Dylan CJ, Tang, Kimberly, Owens, Trenton K, Krishnappa, Netravathi, Sachdeva, Rohan, Barrangou, Rodolphe, Deutschbauer, Adam M, Banfield, Jillian F, Doudna, Jennifer A

Source: Nature Microbiology. 7(1)

Subject Terms: 3107 Microbiology (for-2020), 31 Biological Sciences (for-2020), 3103 Ecology (for-2020), 3105 Genetics (for-2020), Biotechnology (rcdc), Genetics (rcdc), Microbiome (rcdc), Human Genome (rcdc), 1.1 Normal biological development and functioning (hrcs-rac), 2.2 Factors relating to the physical environment (hrcs-rac), Infection (hrcs-hc), Archaea (mesh), Bacteria (mesh), CRISPR-Cas Systems (mesh), Gastrointestinal Microbiome (mesh), Gene Editing (mesh), Genome, Bacterial (mesh), Humans (mesh), Infant (mesh), Microbial Consortia (mesh), RNA, Guide, CRISPR-Cas Systems (mesh), Soil Microbiology (mesh), Humans (mesh), Bacteria (mesh), Archaea (mesh), Soil Microbiology (mesh), Genome, Bacterial (mesh), Infant (mesh), Microbial Consortia (mesh), CRISPR-Cas Systems (mesh), Gastrointestinal Microbiome (mesh), Gene Editing (mesh), RNA, Guide, CRISPR-Cas Systems (mesh), Archaea (mesh), Bacteria (mesh), CRISPR-Cas Systems (mesh), Gastrointestinal Microbiome (mesh), Gene Editing (mesh), Genome, Bacterial (mesh), Humans (mesh), Infant (mesh), Microbial Consortia (mesh), RNA, Guide, CRISPR-Cas Systems (mesh), Soil Microbiology (mesh), 0605 Microbiology (for), 1108 Medical Microbiology (for), 3107 Microbiology (for-2020)

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/3qr0g3mh
https://escholarship.org/content/qt3qr0g3mh/qt3qr0g3mh.pdf

A widespread group of large plasmids in methanotrophic Methanoperedens archaea

Authors: Schoelmerich, Marie C, Ouboter, Heleen T, Sachdeva, Rohan, Penev, Petar I, Amano, Yuki, West-Roberts, Jacob, Welte, Cornelia U, Banfield, Jillian F

Source: Nature Communications. 13(1)

Subject Terms: Biotechnology, Genetics, Archaea, Anaerobiosis, Methane, Oxidation-Reduction, Plasmids

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/16t3s24j
https://escholarship.org/content/qt16t3s24j/qt16t3s24j.pdf

Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria

Authors: Jaffe, Alexander L, Thomas, Alex D, He, Christine, Keren, Ray, Valentin-Alvarado, Luis E, Munk, Patrick, Bouma-Gregson, Keith, Farag, Ibrahim F, Amano, Yuki, Sachdeva, Rohan, West, Patrick T, Banfield, Jillian F

Source: mBio. 12(4)

Subject Terms: Human Genome, Genetics, Biotechnology, Animals, Bacteria, Ecosystem, Evolution, Molecular, Genome, Bacterial, Genomics, Metagenome, Phylogeny, RNA, Ribosomal, 16S, CPR bacteria, animal microbiome, bacterial evolution, comparative genomics, habitat transition, Microbiology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/59f9v582
https://escholarship.org/content/qt59f9v582/qt59f9v582.pdf

Closely related Lak megaphages replicate in the microbiomes of diverse animals

Authors: Crisci, Marco A, Chen, Lin-Xing, Devoto, Audra E, Borges, Adair L, Bordin, Nicola, Sachdeva, Rohan, Tett, Adrian, Sharrar, Allison M, Segata, Nicola, Debenedetti, Francesco, Bailey, Mick, Burt, Rachel, Wood, Rhiannon M, Rowden, Lewis J, Corsini, Paula M, van Winden, Steven, Holmes, Mark A, Lei, Shufei, Banfield, Jillian F, Santini, Joanne M

Source: iScience. 24(8)

Subject Terms: Genetics, Human Genome, Microbiome, Omics, Virology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/5qg3r9kp
https://escholarship.org/content/qt5qg3r9kp/qt5qg3r9kp.pdf

Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes

Authors: Huddy, Robert J, Sachdeva, Rohan, Kadzinga, Fadzai, Kantor, Rose S, Harrison, Susan TL, Banfield, Jillian F

Subject Terms: Microbiology, Biological Sciences, thiocyanate, bioremediation, microbiome, metagenomics, pollution, Environmental Science and Management, Soil Sciences, Medical microbiology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/7fh9534b
https://escholarship.org/content/qt7fh9534b/qt7fh9534b.pdf

Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus

Authors: Ehrenberg, Alexander J, Moehle, Erica A, Brook, Cara E, Doudna Cate, Andrew H, Witkowsky, Lea B, Sachdeva, Rohan, Hirsh, Ariana, Barry, Kerrie, Hamilton, Jennifer R, Lin-Shiao, Enrique, McDevitt, Shana, Valentin-Alvarado, Luis, Letourneau, Kaitlyn N, Hunter, Lauren, Keller, Amanda, Pestal, Kathleen, Frankino, Phillip A, Murley, Andrew, Nandakumar, Divya, Stahl, Elizabeth C, Tsuchida, Connor A, Gildea, Holly K, Murdock, Andrew G, Hochstrasser, Megan L, O’Brien, Elizabeth, Ciling, Alison, Tsitsiklis, Alexandra, Worden, Kurtresha, Dugast-Darzacq, Claire, Hays, Stephanie G, Barber, Colin C, McGarrigle, Riley, Lam, Emily K, Ensminger, David C, Bardet, Lucie, Sherry, Carolyn, Harte, Anna, Nicolette, Guy, Giannikopoulos, Petros, Hockemeyer, Dirk, Petersen, Maya, Urnov, Fyodor D, Ringeisen, Bradley R, Boots, Mike, Doudna, Jennifer A

Source: PLOS ONE. 16(5)

Subject Terms: Infectious Diseases, Biodefense, Emerging Infectious Diseases, Clinical Research, Vaccine Related, Prevention, Good Health and Well Being, Adult, Aged, COVID-19, COVID-19 Testing, Female, Humans, Male, Middle Aged, Program Evaluation, RNA, Viral, Reverse Transcriptase Polymerase Chain Reaction, SARS-CoV-2, Saliva, Social Norms, Surveys and Questionnaires, Universities, Young Adult, IGI SARS-CoV-2 Testing Consortium, General Science & Technology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/7q50s033
https://escholarship.org/content/qt7q50s033/qt7q50s033.pdf

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

Authors: Sieradzki, Ella T, Koch, Benjamin J, Greenlon, Alex, Sachdeva, Rohan, Malmstrom, Rex R, Mau, Rebecca L, Blazewicz, Steven J, Firestone, Mary K, Hofmockel, Kirsten S, Schwartz, Egbert, Hungate, Bruce A, Pett-Ridge, Jennifer

Source: mSystems. 5(4)

Subject Terms: Biological Sciences, Ecology, Bioengineering, Generic health relevance, stable isotope probing, environmental microbiology, experimental design, metagenomics, microbial communities, microbial ecology, qSIP, statistical power

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/0xq0896w
https://escholarship.org/content/qt0xq0896w/qt0xq0896w.pdf