Assistant Professor Amanda Alker<\/a> is working to change the way scientists manipulate bacteria DNA, helping build a new field of microbiome editing.<\/p>\n\n\n\n\u201cAntibiotics indiscriminately kill all the bacteria in your gut, including the ones that help us digest our nutrients and protect us,\u201d Alker said. \u201cWhat if in the future microbiome editing could be used as a targeted therapeutic that could reduce the need for antibiotics? The promise is there, but significant foundational work needs to be done before that dream can be realized. We\u2019re setting the groundwork for what is the dawn of a new field.\u201d<\/p>\n\n\n\n
While classical approaches in bacterial genetics require isolating bacteria from their natural environment to perform DNA manipulations, a promising new technology called CRISPR-associated Transposons (CASTs) enables microbiome editing through precision edits tailored to target bacterial species and even the specific genes that are causing disease. The Alker Lab is focused on adapting CASTs to target new bacteria and identify strategies for DNA editing and enrichment that do not rely on the delivery of antibiotic resistance genes, and do not destroy the rest of a microbiome.<\/p>\n\n\n\n
\u201cMy work is broken down broadly into understanding how bacteria interact with the environment and cause disease, or how they protect against disease,\u201d Alker said. \u201cTo manipulate them often required changing the genome of the bacteria to understand how they function. Now we can get a really good understanding of where our bad bugs are and how they\u2019re behaving in the microbiome, which was never possible before because we\u2019ve always had to take the bacteria out of its environment to do these kinds of manipulations. We\u2019re excited to bring microbiome editing with these new CRISPR technologies to different disease systems for the first time.\u201d<\/p>\n\n\n\n
The microbiome editing tools Alker is developing can also benefit the natural environment and help contribute to the Blue Economy vital to Rhode Island\u2019s financial future.<\/p>\n\n\n\n
Oysters are a popular regional food source but can cause gastrointestinal issues for some because of a bacteria called Vibrio that lives in them, especially during warmer months. Alker\u2019s lab is working to develop short DNA codes that can target harmful bacteria using CASTs while leaving the rest of the microbiome\u2014in this case, an oyster\u2014untouched. Oysters are a great model system for her research, Alker said, because while scientists know the identity of the disease-causing bacteria, preventative antibiotic treatment is not an option for the aquaculture industry due to the spread of antibiotic resistance. Her lab can grow oysters in controlled tanks to avoid biocontainment concerns, especially while performing foundational work to validate the approach.<\/p>\n\n\n\n
Alker is also interested in working in this system because it takes advantage of oysters\u2019 filter-feeding behavior. By adding DNA editing tools to the water in an aquaculture system, the oysters will naturally ingest them, delivering the tool to the target bacteria to break the DNA that makes people sick, but not touching any of the other bacteria within the microbiome.<\/p>\n\n\n\n
\u201cWhat if we could provide an intervention so you don\u2019t get sick when you eat your beloved oysters?\u201d Alker said. \u201cWe\u2019re doing this proof of concept in oyster aquaculture to show that microbiome editing can be used to prevent and control diseases. To understand and control some of the diseases or the therapeutics we\u2019re interested in studying, we want to develop genetic engineering tools tailored to those particular bacteria. Once we prove we can get this system running, the opportunities are endless.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"
KINGSTON, R.I. \u2014 May 15, 2026 \u2014 Whenever a patient presents with gastrointestinal illness caused by bacteria, the common response is to prescribe an antibiotic that kills the disease-causing bacteria, allowing the immune system to quell the symptoms and helping the patient recover. The problem is antibiotics are almost too good at their job. In […]<\/p>\n","protected":false},"author":25,"featured_media":108879,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[2],"tags":[41,1905],"class_list":["post-108878","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-archives","tag-college-of-pharmacy","tag-research"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts\/108878","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/users\/25"}],"replies":[{"embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/comments?post=108878"}],"version-history":[{"count":1,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts\/108878\/revisions"}],"predecessor-version":[{"id":108880,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts\/108878\/revisions\/108880"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/media\/108879"}],"wp:attachment":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/media?parent=108878"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/categories?post=108878"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/tags?post=108878"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}