WELCOME TO THE RAMIREZ LAB
Full fathom five, thy father lies;
Of his bone are coral made;
Those are pearls that were his eyes:
Nothing of him that doth fade,
But doth suffer a sea-change
Into something rich and strange
Microbial Eco-genomics @ CalStateLA
We are engaged in interdisciplinary investigations that integrate ecology and genomics to study the diversity, distribution, and functioning of microbial communities in nature. This involves high-throughput molecular sequencing merged with environmental metadata analyzed using high-performance computing. Our work is at the nexus of basic science and applications in conservation biology, environmental monitoring, and biotechnology.
Octopus Odyssey Expeditions
Our two 2023 oceanographic expedition legs onboard the amazing Schmidt Ocean Institute’s Research Vessel (RV) Falkor too with the Remotely Operated Submersible (ROV) Subastian were a blast! After weeks at sea exploring the microbiology of seafloor octopus nurseries as part of an international, multi-disciplinary, scientific team our lab successfully deployed and collected 6-month microbial colonization experiments across Costa Rica’s Pacific seamount complex known as “La Pampa Submarina”. Hundreds of natural sediment and rock samples from this seamount network were also collected. Check out some exciting footage from this work courtesy of the Schmidt Ocean Institute below:
Octopus Odyssey 2023 Expedition: Week 1 Summary.
Octopus Odyssey 2023 Expedition: Science focus on Dr. Ramírez.
Octopus Odyssey 2023 Expedition: HD Highlights.
Octopus Odyssey 2023 Expedition: Week 3 Summary, 2023 Leg 1 Sign Off.
Major lab themes
Long-term microbial colonization experiment deployed at a deep-sea Octopus nursery on the southern slopes of El Dorado Hill (~3,000m or 9,000ft water depth), located in Costa Rica’s Pacific seamount network, La Pampa Submarina. Courtesy of Schmidt Ocean Institute.
Subseafloor Life
The ocean subseafloor hosts a sizable fraction of the Earth's microbes and plays a major role in the global carbon cycle. Understanding the Planetary-level repercussions of life beneath the seafloor, specifically, in marine sediment and sediment-buried crust, the most inaccessible environments on Earth, is important to understanding the environmental limits of life and co-evolution of Earth's biosphere and geosphere.
Animal-Microbe Interactions
Animal-microbe interactions are key determinants of animal health and development and, consequently, ecosystem functioning. Our work on host-microbiome interaction involves two distinct but important models: marine sponges and poultry. Marine sponges represent the most ancient lineage of animal hosted microbiomes. Our recent work shows novel symbiosis activities involving carbon cycling these marine animals. Our poultry microbiome work aims to develop functional probiotic technologies using experimental and large data mining (multi-terabyte) approaches to survey the chicken GI tract for microbial activity, metabolite profiles, and, ultimately, emergent host phenotypic effects .
Lab Members
Gustavo A. Ramírez
https://orcid.org/0000-0001-8122-4898
Principal Investigator.
Dr. Ramírez is a biophile. That is, he is insatiably curious about life (oddest thing ever!) and spends his time understanding its structure, function, evolution, emergence and potential plurality on Earth, an ocean world, and other oceans worlds in the Solar System and beyond. This pursuit has led Dr. Ramírez to the bottom of the sea and, considering life as an emergent physical property of information (DNA), often also leads him to excursions into uncharted digital depths. Accordingly, his research involves, in addition to oceanographic fieldwork, high-performance computing as a complementary vessel for exploring life’s deepest secrets patiently awaiting discovery in biological information.
Shiva Sadeghpour
https://orcid.org/0000-0001-8122-4898
2023 NIH LABB PhD Graduate Fellow
Shiva is a passionate biologist who is driven by her fascination with understanding the interactions between living things and the environment. She earned her Bachelor's degree in Biological Science from UC Irvine and is currently pursuing her Master's degree in Dr. Ramirez's lab. Her research focuses on using computational biology and bioinformatics to study tiny microorganisms at the bottom of the ocean. Recently, she has become interested in learning more about Candidatus Desulforudis audaxviator (CDA), a species with a conserved genome and a keystone species in areas like South Africa and West Siberia. Shiva and Dr. Ramirez have hypothesized that there may be more species that shape CDA as a community member rather than a dominant, clonal, lineage. In her free time, Shiva enjoys playing with her 3D printer, playing volleyball in the park, camping, and kayaking in reservoirs. She is excited to continue her studies in bioinformatics and unravel the mysteries of the natural world.
Manuel Oscar Almacen
https://orcid.org/0000-0001-8122-4898
Graduate Student.
Oscar is a Microbiology undergraduate student researcher in the Ramírez lab. He has been recently accepted to the Masters in Biology program and will continue studies in Microbial Ecology and Bioinformatics under the guidance of Dr. Ramírez. Oscar considers himself “eternally curious”; a trait that he is sure will serve him well in his current and future scientific pursuits. Lastly, Oscar is a casual Chess player (unrated) and a big fan of competitive Dota 2.
Dyanna Jiménez
Undergraduate Student
Dyanna is a 3rd year Biology/Microbiology student interested in the effects of spaceflight on microorganisms and the microbiology of wetlands and peatlands. Her hobbies include playing Red Dead Redemption 2, sewing, camping, and drinking coffee. Dyanna is a very curious and analytical person and looks forward to using bioinformatics to analyze and quantify data.
Fernando Paz Melchor
Undergraduate Student
Fernando is a biology student who enjoys exploring the outdoors and learning about the complexities of nature and the universe.
Alexis Nebrenski-Farias
Undergraduate Student
Alexis is a senior majoring in Biology with a general option. Their interests range from Neurobiology to Medical Microbiology. They are interested in anything Microbiology and are fascinated with the omnipresence and influence of microbes in the universe. Alexis’s hobbies include playing guitar, building Legos, and playing video games.
Alec Milbourne
Undergraduate Student (Volunteer)
Alec is a senior Chemistry/Bioinformatics student interested in pursuing a graduate education in Ecology and Forestry. His general hobbies revolve around spending time outdoors camping or looking for local wild edibles to cook with. He is a lover of coffee and the life sciences, and is looking forward to gaining practical experience in the field of Bioinformatics.
Micheal Zitser
Undergraduate Student (Volunteer)
Michael is a senior majoring in Biochemistry and minoring in Art interested in the human microbiome. He is interested in microbiology, computational biology, and organic chemistry research. His hobbies include art, in which he has an award-winning portfolio recognized by the Scholastic Art and Writing Awards and acts as volunteer instructor for children with chronic illnesses.
Isabella Vahrson (former lab member)
https://orcid.org/0000-0003-2650-4103
Graduate Student. MS, 2022.
Isabella is a neuroscientist turned bioinformatician, with a background in neuroinflammation and neuroendocrinology from the University of California, Riverside. Isabella’s project involved large-scale data mining and analysis using applied AI to track the prevalence and diversity of hydrogenotrophic methanogenic archaea in the chicken gastrointestinal tract. Her multi-terabyte, study revealed the presence and diversity of gut methanogenic archaea and identified several novel methanogenic sequences expanding our understanding of carbon cycling and feed-conversion energetics in poultry. These findings place importance on methanogens for the regulation of chicken health and productivity. Overall, this work has major implications for global food production, as chicken is the most consumed protein worldwide.
Xiuhnel Zein (former lab member)
Undergraduate Student, Fall 2023
Xiuhnel is a senior working towards a BS in biology. Her plans are to pursue Medical School after graduation, however, her interests are far ranging and include other facets of biology and aerospace engineering. Overall, she is passionate about everything that has life. Xiuhnel’s other activities include a deep joy from painting and traveling.
Angel Meza
Former Undergraduate Student (Spring 2024)
Angel is finishing the last year of his bachelors in Microbiology degree. After graduating he wants to continue his education by working towards a Masters of Science with a focus on cancer pathology. He’s passionate about dealing with microorganisms. Angel is an avid amateur mycologist. He takes pleasure in growing different species of mushrooms and enjoys exploring their unique biology and their interactions with humanity and other parts of nature.
Lab News
Summer 2024 - Fernando and Alexis join the lab!
Spring 2024 - Dyanna and Gissele join the lab!
Fall 2023 - Schmidt Ocean Institute cruise to El Dorado Seamount, Octopus Odyssey too Expedition
https://schmidtocean.org/cruise/octopus-odyssey-too/
Fall 2023 - Shiva is selected as an NIH LABB Ph.D. Fellow! Congratulations!!!
Summer 2023 - Dyanna, Angel, and Xiuhnel join the lab! Welcome!
Summer 2023 - The lab will host NASA’s Gene Lab for University Summer Bioinformatics Bootcamp https://genelab.nasa.gov/genelab-universities-gl4u.
Summer 2023 - Schmidt Ocean Institute cruise to El Dorado Seamount, Octopus Odyssey Expedition https://schmidtocean.org/cruise/octopus-odyssey/.
Summer 2023 - Shiva joins the lab as a graduate student.
Summer 2023 - Oscar joins the lab as a graduate student.
Spring 2023 - Eagle1 server goes live.
Fall 2022 - Oscar joins the lab as an undergraduate researcher.
Summer 2022 - The lab relocates to the Department of Biological Sciences at the California State University, Los Angeles.
Spring 2022- Isabella recruited as a data scientist by Rosalind! Upon graduation from Western University’s Graduate College of Biomedical Sciences in May, Isabella will leave the Ramírez lab to continue to pursue her passion for bioinformatics and big data analysis at ROSALIND, a software biotech company in San Diego, as part of their data science and AI team. -Congratulations!
Spring 2022- Isabella successfully defends her Master’s thesis.
Spring 2021 - Isabella V. joins the lab to pursue a M.S. degree.
Spring 2021 - The Ramírez lab is established at the College of Veterinary Medicine, Western University of Health Sciences, Pomona.
Peer -Reviewed Publications
Ramírez, Hoffmann, Lee, et al. 2016
Ramírez, Keshri, Vahrson, et al. 2022
2024
26*. Ramírez, GA and Mel, GC. Distribution-driven disturbance of a molecular community: a theoretical framework. bioRxiv: https://www.biorxiv.org/content/10.1101/2024.03.11.584481v1.full.pdf *-preprint
25. Ferreira, C, Burgsdorf, I, Perez, T, Ramírez, GA, et al. Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis. Microbiome, in press..
24. Ramírez, GA, Paraskevi Mara, David Beaudoin, Diana Bojanova, John E. Hinkle, Brewster Kingham, Virginia P. Edgcomb, Yuki Morono, Andreas Teske. The DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and re-defined limits in bulk extractions of nucleic acids from deep marine sediments. doi: http://publications.iodp.org/proceedings/385/204/385_204.html
23. Guan, J, Ramírez, GA, Eng, C, Oakley, BB. 2024. Microbiome resilience of three-toed box turtles (Terrapene carolina triunguis) in response to rising temperatures. https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2024.1276436/full
22. Garber, AI, Ramírez, GA, D’Hondt, S. 2024. Genomic Stasis over millions of years in marine sediment. Envir. Microbiol. https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16674?af=R
2023
21. Ramírez GA, Bar-Shalom, R, Furlan, A, Romeo, R, Gavagnin, M, Calabrese, G, Garber, AI, Steindler L. 2023. Bacterial aerobic methane cycling by the marine sponge-associated microbiome. Microbiome 11, 49 (2023). https://doi.org/10.1186/s40168-023-01467-4.
2022
20. Weinroth, MD, Oakley, BB, Ramírez, GA, et al., 2022. 16S rRNA gene-based assessment of common broiler chicken sampling methods: evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations. Front. Physiol., doi: 10.3389/fphys.2022.996654.
19. Ramírez, GA, Keshri, J, Vahrson, I, Garber, AI, Berrang, ME, Cox, NA, González-Cerón, F, Aggrey, SE, Oakley, BB, et al. 2022. Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens. Front. Vet. Sci. doi: 10.3389/fvets.2022.904698.
18. Weinroth, MD, Belk, AD, Dean, C, Noyes, N, Dittoe, DK, Rothrock, MJ, Ricke, SC, Myer, PR, Henninger, MT, Ramírez, GA, Oakley, BB, et al. 2022. Considerations and Best Practices in Animal Science 16S rRNA gene sequencing Microbiome Studies. Journal of Animal Science. https://doi.org/10.1093/jas/skab346.
2021
17. Garber, AI, Zehnpfennig, JR, Sheik, CS, Henson, MW, Ramírez, GA, Mahon, AR, Halanych, KM, Learman, DR. 2021. Metagenomic survey of Antarctic marine sediment. mSphere Journal 6 (6) e00770-21. https://doi.org/10.1128/mSphere.00770-21.
16. Ramírez GA, Paraskevi VM, Edgcomb VA, Teske AP. 2021. Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California. PLOS ONE 16 (9): e0256321. https://doi.org/10.1371/journal.pone.0256321
15. Garber AI*, Ramírez GA*, McAllister S, Orsi W, D’Hondt S. 2021. Cryptic metabolisms in deep anoxic marine sediment. Envir. Microbiol. doi:10.1111/1758-2229.12983.
14. Teske A, Amilis A, Ramírez GA, Reysenbach, AL. 2021. Archaea in the environment: views on archaeal distribution, activity, and biogeography. Front. Microbiol. -Extreme Microbiology. doi: 10.3389/fmicb.2021.667596.
13. Garber AI, Cohen AB, Nealson KH, Ramírez GA, Barco RA, Merino N. 2021. Metagenomic insights into the microbial iron cycle of subseafloor habitats. Front. Microbiol. doi: 10.3389/fmicb.2021.667944.
2020
12. Ramírez GA, Richardson E, Clark J, Keshri, J, Drechsler, Y, Berrang, ME, Meinersmann, RJ, Cox, NA, Oakley BB. 2020. Broiler Chickens and Early Life Programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects. PLoS ONE 15 (11): e0242108. https://doi.org/10.1371/journal.pone.0242108.
11. Ramírez GA, McKay L.J., Fields, M.W., Ravelo, A.C., Teske, A.P. 2020. The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories. iScience Journal. Vol 23, Issue 9: https://doi.org/10.1016/j.isci.2020.101459.
10. Zhao, R., Dahle, H., Ramírez, G.A., Jørgensen, S.L. 2020. Indigenous Ammonia Oxidizing Archaea in Anoxic Subseafloor Oceanic Crust. mSystems J. Volume 5. Issue 2: e00758-19.doi: 10.1128/mSystems.00758-19.
2019
9. Teske, A., MacKay, L., Ravelo, A.C., Aiello, I., Mortera, C., Núñez-Useche, F., Chanton, J., Brunner, B., Hensen, C., Ramírez, G.A., et al. 2019. Characteristics and evolution of sill-driven hydrothermalism on the Guaymas Basin ridge flanks – the Ringvent site. Sci.Reports. 9:13847. doi: https://doi.org/10.1038/s41598-019-50200-5.
8. Ramírez GA, Garber AI, Lecoeuvre A, D’Angelo T, Wheat CG, Orcutt BN. 2019. Ecology of Subseafloor Crustal Biofilms. Front. Microbiol. -Extreme Microbiology. doi: 10.3389/fmicb.2019.01983.
2018
7. Ramírez GA, Zhao R, Jørgensen SL, D’Hondt S. 2018. Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities. Front. Microbiol. -Extreme Microbiology. doi: 10.3389/fmicb.2018.02969.
6. Ramírez GA, Graham D, D’Hondt S. 2018. Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment. Limnology and Oceanography Methods. Volume 16. Issue 9. doi: 10.1002/lom3.10264.
2017
5. Barco RA, Hoffman, C., Ramírez, GA, Toner, BM, Edwards, KJ, Sylvan, JB. 2017. In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira. Environmental Microbiology Journal. doi: 10.1111/1462-2920.13666.
2016
4. Ramírez GA, Hoffman CL, Lee MD, Lesniewski RA, Barco RA, Garber AI, Toner BM, Wheat CG, Edwards KJ, Orcutt, BN. 2016. Marine Microbial Induced Corrosion Monitored at Santa Catalina Island, California. Front. Microbiol. Biogeochemistry and Geomicrobiology. doi: 10.3389/fmicb.2016.01679.
3. Baquiran J-PM*, Ramírez GA*, Haddad AG, Toner BM, Hulme S, Wheat CG, Edwards KJ and Orcutt BN. 2016. Temperature and Redox Effect on Mineral Colonization in Juan de Fuca Ridge Flank Subsurface Crustal Fluids. Front. Microbiol. 7:396. doi: 10.3389/fmicb.2016.00396.
2015
2. Barco RA, Emerson D, Sylvan JB, Orcutt BN, Jacobson Meyers ME, Ramírez GA, Zhong JD, Edwards KJ. 2015. New insight into microbial iron oxidation as revealed by the proteomic profile of an obligate iron-oxidizing chemolithoautotroph. Appl Environ Microbiol 81:5927–5937.
2012
1. Fisher, AT, Tsuji, T, Petronotis, K, Wheat, CG, Becker, K, Clark, JF, Cowen, J, Edwards, K, Jannasch, H. 2012. IODP Expedition 327 and Atlantis Expedition AT18-07: Observatories and Experiments on the Eastern Flank of the Juan de Fuca Ridge. Scientific Drilling. No. 13: 4-11.