Publications
PUBLICATIONS BY UBIOME STAFF
- Maureen Hitschfeld, Elena Tovar, Sarah Gupta, Elisabeth M. Bik, Christina Palmer, Michael C. Hoaglin, Daniel E. Almonacid, Jessica Richman and Zachary S. Apte.?The role of a sequencing-based clinical intestinal screening test in patients at high-risk for Clostridium difficile and other pathogens: a case report.?Journal of Medical Case Reports?13:9. January 2019.
- Sarah Gupta, Christina Palmer, Elisabeth M. Bik, Juan P. Cardenas, Harold Nu?ez, Laurens Kraal, Sara Bird, Jennie Bowers, Alison Smith, Nathaniel A. Walton, Audrey D. Goddard, Daniel E. Almonacid, Susan Zneimer, Jessica Richman, Zachary S. Apte. Self-Sampling for Human Papillomavirus Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs. Frontiers in Public Health (6):77.April 2018.
- Elisabeth M. Bik, Sara W. Bird, Juan P. Bustamante, Luis E. Leon, Pamela A. Nieto, Kwasi Addae, Víctor Alegría-Mera, Cristian Bravo, Denisse Bravo, Juan P. Cardenas, Glenn A. Carson, Adam Caughey, Paulo C. Covarrubias, José Pérez-Donoso, Graham Gass, Sarah L. Gupta, Kira Harman, Donna Marie B. Hongo, Juan C. Jiménez, Laurens Kraal, Felipe Melis-Arcos, Eduardo H. Morales, Amanda Morton, Camila F. Navas, Harold Nu?ez, Eduardo Olivares, Nicolás órdenes-Aenishanslins, Francisco J. Ossandon, Richard Phan, Raul Pino, Katia Soto-Liebe, Ignacio Varas, Patricia Vera-Wolf, Nathaniel A. Walton, Daniel E. Almonacid, Audrey D. Goddard, Juan A. Ugalde, Susan Zneimer, Jessica Richman, Zachary S. Apte. A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.?PLoS One. May 2019.
- Elisabeth Bik, Juan A. Ugalde, Jon Cousins, Audrey D. Goddard, Jessica Richman, Zachary Apte.?Microbial biotransformations in the human distal gut.?British Journal of Pharmacology. DOI: 10.1111/bph.14085.
- Alejandro Gran-Scheuch, Edwar Fuentes, Denisse M. Bravo, Juan Cristobal Jimenez, Jose M. Pérez-Donoso.?Isolation and characterization of phenanthrene degrading bacteria from diesel fuel-contaminated Antarctic Soils.?Front. Microbiol?8:1634. August 2017.
- Daniel E. Almonacid, Laurens Kraal, Francisco J. Ossandon, Yelena V. Budovskaya, Juan Pablo Cardenas, Elisabeth M. Bik, Audrey D. Goddard, Jessica Richman, Zachary S. Apte.?16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.?PLoS One?12(5): e0176555. May 2017.
- Elisabeth M. Bik, Audrey D. Goddard, Daniel E. Almonacid, Zachary S. Apte.?A gut check at the doctor.?The Biochemist.?April 2017.
- Harold Nu?ez, Ana Moya-Beltrán, Paulo C. Covarrubias, Francisco Issotta, Juan Pablo Cárdenas, Mónica González, Joaquín Atavales, Lillian G. Acu?a, D. Barrie Johnson, and Raquel Quatrini.?Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon.?Front. Microbiol.?January 2017.
- Elisabeth M. Bik.?Friends for Life: Human Microbiota,?Dutch Journal of Medical Microbiology.?December 2016.
PUBLICATIONS USING UBIOME’S TECHNOLOGIES
- K. Scott Weber, Laura C. Bridgewater, Jamie L. Jensen, Donald P. Breakwell, Brent L. Nielsen, Steven M. Johnson?Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses PLoS ONE 13(4): e0193696, April 2018.
- Dustin D. Heeney, Mélanie G. Gareau, Maria L. Marco.?Intestinal Lactobacillus in health and disease, a driver or just along for the ride??Curr Opin Biotechnol., Volume 49:140-147, 2018.
- Ryan H. Hsu, ?Dylan M. McCormick, ?Mitchell Lee J. Seitz Jr., Lauren M. Lui, Harneet S. Rishi, Adam P. Arkin.?An interventional Soylent diet increases the Bacteroidetes to Firmicutes ratio in human gut microbiome communities: a randomized controlled trial.?bioRxiv?200881.
- Jason R. Anderson, Ian Carroll, M. Andrea Azcarate-Peril, Amber D. Rochette, Leslie J. Heinberg, Christine Peat, Kristine Steffen, Lisa M. Manderino, James Mitchell, John Gunstad.?A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults.?Sleep Medicine, Volume 38, pages 104-107.
- Lisa Manderino, Ian Carroll, M. Andrea Azcarate-Peril, Amber Rochelette.?Preliminary Evidence for an Association Between the Composition of the Gut Microbiome and Cognitive Function in Neurologically Healthy Older Adults.?J. Intern Neuropsychological Society, Volume 23 Issue 8, June 2017.
- Jessica D. Forbes, Natalie C. Knox, Jennifer Ronholm, Franco Pagotto, Aleisha Reimer. Metagenomics:?The Next Culture-Independent Game Changer.?Front Microbiol, Volume 8:1069, 2017.
- Kodukula Krishna, Faller Douglas V., Harpp David N., Kanara Iphigenia, Pernokas Julie, Pernokas Mark, Powers Whitney R., Soukos Nikolaos S., Steliou Kosta, and Moos Walter H. Gut Microbiota and Salivary Diagnostics: The Mouth Is Salivating to Tell Us Something. BioResearch Open Access. October 2017, 6(1): 123-132.
- Richard Sprague. Fusicatenibacter Is Associated with Kefir Drinking. bioRxiv 218313. November 2017.
FAQs
-
Probiotic Foods: The Good Bugs
When you think of gut health, your mind may jump straight to the word “probiotic.” This isn’t surprising; a Google Trend Report indicated that consumer demand for probiotics has increased significantly since 2004.
Additionally, since the mid-1990s, research has suggested that probiotics may “aid digestion and help maintain gut health.”
What are probiotics?
The World Health Organization defines probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” ?
According to the National Center for Complementary and Integrative Health, probiotics may help your body find the proper balance of microorganisms and “stabilize the digestive tract’s barriers against undesirable microorganisms.”
Probiotic Foods
Probiotics aren’t only available in supplement form. Many delicious foods are naturally full of probiotics!
Yogurt, for example, is produced when a starter culture of bacteria – usually Streptococcus thermophilus and Lactobacillus bulgaricus – ?is added to milk. The bacteria break down the lactose sugars into lactic acid.
Pickling is a time tested technique for preserving vegetables and fruits. While pickling can involve immersing produce in vinegar to kill all the bacteria, a similar outcome can result from immersing produce in salted water for several weeks. In that briny environment, the Lactobacillus bacteria that naturally occurs on produce like cucumbers have a chance to produce lactic acid, which serves as a preservative.
Another common category of probiotic-rich foods is fermented foods. Foods ferment when molds, yeasts, or bacteria produce enzymes that break down the food into smaller, simpler compounds. The fermented foods are often abundant in probiotic bacteria, such as Lactobacillus, Bifidobacterium, Pediococcus, and Weisella.
Probiotic-rich foods include:
- Yogurt
- Pickles
- Sauerkraut
- Kimchi
- Kombucha
- Miso
- Kvass
- Cottage cheese
- Many more!
Curious if the probiotic bacteria in the food you’re eating is making its way to your gut?
Explorer? identifies microbes found in the most common probiotic foods and lets you see how your levels of these microbes compare to others who consume these foods.
Use the code UNLEASH at checkout to get 50% off a Gut Explorer kit through the end of February 2019.
If you’ve used Explorer and have a story to tell, we’d love to hear from you! Share your story on social tagging @ubiome and #UnleashYourExplorer. You’ll be entered for the chance to win 1 Gut Explorer kit each week during February and for the Grand Prize Drawing: a Gut Time Lapse set.*
*All posts must tag @uBiome?and use #UnleashYourExplorer to be counted as a valid entry.?The?first weekly contest will run Friday 2/1 to Thursday 2/14. Entries must be received by 11:59pm PST on Thursday 2/1.?The?Grand Prize contest will run Friday 2/1 – Thursday 2/28.? Entries must be received by 11:59 PST on Thursday 2/28 for?the?Grand Prize. Weekly winners will be announced at 10:00am PST on Friday 2/15.?The?Grand Prize winner will be announced by 10:00am PST on 3/1/2019.
-
Probiotic Foods: The Good Bugs
When you think of gut health, your mind may jump straight to the word “probiotic.” This isn’t surprising; a Google Trend Report indicated that consumer demand for probiotics has increased significantly since 2004.
Additionally, since the mid-1990s, research has suggested that probiotics may “aid digestion and help maintain gut health.”
What are probiotics?
The World Health Organization defines probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” ?
According to the National Center for Complementary and Integrative Health, probiotics may help your body find the proper balance of microorganisms and “stabilize the digestive tract’s barriers against undesirable microorganisms.”
Probiotic Foods
Probiotics aren’t only available in supplement form. Many delicious foods are naturally full of probiotics!
Yogurt, for example, is produced when a starter culture of bacteria – usually Streptococcus thermophilus and Lactobacillus bulgaricus – ?is added to milk. The bacteria break down the lactose sugars into lactic acid.
Pickling is a time tested technique for preserving vegetables and fruits. While pickling can involve immersing produce in vinegar to kill all the bacteria, a similar outcome can result from immersing produce in salted water for several weeks. In that briny environment, the Lactobacillus bacteria that naturally occurs on produce like cucumbers have a chance to produce lactic acid, which serves as a preservative.
Another common category of probiotic-rich foods is fermented foods. Foods ferment when molds, yeasts, or bacteria produce enzymes that break down the food into smaller, simpler compounds. The fermented foods are often abundant in probiotic bacteria, such as Lactobacillus, Bifidobacterium, Pediococcus, and Weisella.
Probiotic-rich foods include:
- Yogurt
- Pickles
- Sauerkraut
- Kimchi
- Kombucha
- Miso
- Kvass
- Cottage cheese
- Many more!
Curious if the probiotic bacteria in the food you’re eating is making its way to your gut?
Explorer? identifies microbes found in the most common probiotic foods and lets you see how your levels of these microbes compare to others who consume these foods.
Use the code UNLEASH at checkout to get 50% off a Gut Explorer kit through the end of February 2019.
If you’ve used Explorer and have a story to tell, we’d love to hear from you! Share your story on social tagging @ubiome and #UnleashYourExplorer. You’ll be entered for the chance to win 1 Gut Explorer kit each week during February and for the Grand Prize Drawing: a Gut Time Lapse set.*
*All posts must tag @uBiome?and use #UnleashYourExplorer to be counted as a valid entry.?The?first weekly contest will run Friday 2/1 to Thursday 2/14. Entries must be received by 11:59pm PST on Thursday 2/1.?The?Grand Prize contest will run Friday 2/1 – Thursday 2/28.? Entries must be received by 11:59 PST on Thursday 2/28 for?the?Grand Prize. Weekly winners will be announced at 10:00am PST on Friday 2/15.?The?Grand Prize winner will be announced by 10:00am PST on 3/1/2019.
-
Probiotic Foods: The Good Bugs
When you think of gut health, your mind may jump straight to the word “probiotic.” This isn’t surprising; a Google Trend Report indicated that consumer demand for probiotics has increased significantly since 2004.
Additionally, since the mid-1990s, research has suggested that probiotics may “aid digestion and help maintain gut health.”
What are probiotics?
The World Health Organization defines probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” ?
According to the National Center for Complementary and Integrative Health, probiotics may help your body find the proper balance of microorganisms and “stabilize the digestive tract’s barriers against undesirable microorganisms.”
Probiotic Foods
Probiotics aren’t only available in supplement form. Many delicious foods are naturally full of probiotics!
Yogurt, for example, is produced when a starter culture of bacteria – usually Streptococcus thermophilus and Lactobacillus bulgaricus – ?is added to milk. The bacteria break down the lactose sugars into lactic acid.
Pickling is a time tested technique for preserving vegetables and fruits. While pickling can involve immersing produce in vinegar to kill all the bacteria, a similar outcome can result from immersing produce in salted water for several weeks. In that briny environment, the Lactobacillus bacteria that naturally occurs on produce like cucumbers have a chance to produce lactic acid, which serves as a preservative.
Another common category of probiotic-rich foods is fermented foods. Foods ferment when molds, yeasts, or bacteria produce enzymes that break down the food into smaller, simpler compounds. The fermented foods are often abundant in probiotic bacteria, such as Lactobacillus, Bifidobacterium, Pediococcus, and Weisella.
Probiotic-rich foods include:
- Yogurt
- Pickles
- Sauerkraut
- Kimchi
- Kombucha
- Miso
- Kvass
- Cottage cheese
- Many more!
Curious if the probiotic bacteria in the food you’re eating is making its way to your gut?
Explorer? identifies microbes found in the most common probiotic foods and lets you see how your levels of these microbes compare to others who consume these foods.
Use the code UNLEASH at checkout to get 50% off a Gut Explorer kit through the end of February 2019.
If you’ve used Explorer and have a story to tell, we’d love to hear from you! Share your story on social tagging @ubiome and #UnleashYourExplorer. You’ll be entered for the chance to win 1 Gut Explorer kit each week during February and for the Grand Prize Drawing: a Gut Time Lapse set.*
*All posts must tag @uBiome?and use #UnleashYourExplorer to be counted as a valid entry.?The?first weekly contest will run Friday 2/1 to Thursday 2/14. Entries must be received by 11:59pm PST on Thursday 2/1.?The?Grand Prize contest will run Friday 2/1 – Thursday 2/28.? Entries must be received by 11:59 PST on Thursday 2/28 for?the?Grand Prize. Weekly winners will be announced at 10:00am PST on Friday 2/15.?The?Grand Prize winner will be announced by 10:00am PST on 3/1/2019.
-
Probiotic Foods: The Good Bugs
When you think of gut health, your mind may jump straight to the word “probiotic.” This isn’t surprising; a Google Trend Report indicated that consumer demand for probiotics has increased significantly since 2004.
Additionally, since the mid-1990s, research has suggested that probiotics may “aid digestion and help maintain gut health.”
What are probiotics?
The World Health Organization defines probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” ?
According to the National Center for Complementary and Integrative Health, probiotics may help your body find the proper balance of microorganisms and “stabilize the digestive tract’s barriers against undesirable microorganisms.”
Probiotic Foods
Probiotics aren’t only available in supplement form. Many delicious foods are naturally full of probiotics!
Yogurt, for example, is produced when a starter culture of bacteria – usually Streptococcus thermophilus and Lactobacillus bulgaricus – ?is added to milk. The bacteria break down the lactose sugars into lactic acid.
Pickling is a time tested technique for preserving vegetables and fruits. While pickling can involve immersing produce in vinegar to kill all the bacteria, a similar outcome can result from immersing produce in salted water for several weeks. In that briny environment, the Lactobacillus bacteria that naturally occurs on produce like cucumbers have a chance to produce lactic acid, which serves as a preservative.
Another common category of probiotic-rich foods is fermented foods. Foods ferment when molds, yeasts, or bacteria produce enzymes that break down the food into smaller, simpler compounds. The fermented foods are often abundant in probiotic bacteria, such as Lactobacillus, Bifidobacterium, Pediococcus, and Weisella.
Probiotic-rich foods include:
- Yogurt
- Pickles
- Sauerkraut
- Kimchi
- Kombucha
- Miso
- Kvass
- Cottage cheese
- Many more!
Curious if the probiotic bacteria in the food you’re eating is making its way to your gut?
Explorer? identifies microbes found in the most common probiotic foods and lets you see how your levels of these microbes compare to others who consume these foods.
Use the code UNLEASH at checkout to get 50% off a Gut Explorer kit through the end of February 2019.
If you’ve used Explorer and have a story to tell, we’d love to hear from you! Share your story on social tagging @ubiome and #UnleashYourExplorer. You’ll be entered for the chance to win 1 Gut Explorer kit each week during February and for the Grand Prize Drawing: a Gut Time Lapse set.*
*All posts must tag @uBiome?and use #UnleashYourExplorer to be counted as a valid entry.?The?first weekly contest will run Friday 2/1 to Thursday 2/14. Entries must be received by 11:59pm PST on Thursday 2/1.?The?Grand Prize contest will run Friday 2/1 – Thursday 2/28.? Entries must be received by 11:59 PST on Thursday 2/28 for?the?Grand Prize. Weekly winners will be announced at 10:00am PST on Friday 2/15.?The?Grand Prize winner will be announced by 10:00am PST on 3/1/2019.