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VAM Scholarships Available
Students and trainees can get financial help to attend the Vascular Annual Meeting in June. The Society for Vascular Surgery distributes dozens of travel scholarships to attend VAM, which is the perfect opportunity to meet other students as well as other members and leaders of the vascular surgical community. Recipients are eligible to receive complimentary meeting registration plus a travel scholarship. Two award categories are available, the General Surgery Resident/Medical Student Travel Scholarship and the Diversity Medical Student Travel Scholarship. Apply today.
Students and trainees can get financial help to attend the Vascular Annual Meeting in June. The Society for Vascular Surgery distributes dozens of travel scholarships to attend VAM, which is the perfect opportunity to meet other students as well as other members and leaders of the vascular surgical community. Recipients are eligible to receive complimentary meeting registration plus a travel scholarship. Two award categories are available, the General Surgery Resident/Medical Student Travel Scholarship and the Diversity Medical Student Travel Scholarship. Apply today.
Students and trainees can get financial help to attend the Vascular Annual Meeting in June. The Society for Vascular Surgery distributes dozens of travel scholarships to attend VAM, which is the perfect opportunity to meet other students as well as other members and leaders of the vascular surgical community. Recipients are eligible to receive complimentary meeting registration plus a travel scholarship. Two award categories are available, the General Surgery Resident/Medical Student Travel Scholarship and the Diversity Medical Student Travel Scholarship. Apply today.
Surgeons: Urge PAs to Join SVS
The SVS has a section dedicated solely to vascular physician assistants. All surgeons are encouraged to urge their PAs to join the section. This “professional home” for PAs has grown to 138 members in just one short year and more are always welcome. Benefits include PA-specific education at the Vascular Annual Meeting, leadership development, networking and mentoring opportunities, discounts on SVS events and our JVS subscription and more. Membership applications are processes quarterly. 2019 deadlines are March 1, June 1, Sep. 1 and Dec. 1. Learn more about the PA Section here.
The SVS has a section dedicated solely to vascular physician assistants. All surgeons are encouraged to urge their PAs to join the section. This “professional home” for PAs has grown to 138 members in just one short year and more are always welcome. Benefits include PA-specific education at the Vascular Annual Meeting, leadership development, networking and mentoring opportunities, discounts on SVS events and our JVS subscription and more. Membership applications are processes quarterly. 2019 deadlines are March 1, June 1, Sep. 1 and Dec. 1. Learn more about the PA Section here.
The SVS has a section dedicated solely to vascular physician assistants. All surgeons are encouraged to urge their PAs to join the section. This “professional home” for PAs has grown to 138 members in just one short year and more are always welcome. Benefits include PA-specific education at the Vascular Annual Meeting, leadership development, networking and mentoring opportunities, discounts on SVS events and our JVS subscription and more. Membership applications are processes quarterly. 2019 deadlines are March 1, June 1, Sep. 1 and Dec. 1. Learn more about the PA Section here.
Nominate an Outstanding Surgeon for the Community Excellence Award
This year, the Society for Vascular Surgery will recognize a member in community practice who excels, leads and contributes. If you know of such a surgeon, make your nominations for the SVS Excellence in Community Service Award by Feb. 1. The first recipient will be announced at the 2019 Vascular Annual Meeting in June. Applicants must have a minimum of 20 years as a practicing vascular surgeon and a minimum of five years as an SVS member. Learn more about the award here.
This year, the Society for Vascular Surgery will recognize a member in community practice who excels, leads and contributes. If you know of such a surgeon, make your nominations for the SVS Excellence in Community Service Award by Feb. 1. The first recipient will be announced at the 2019 Vascular Annual Meeting in June. Applicants must have a minimum of 20 years as a practicing vascular surgeon and a minimum of five years as an SVS member. Learn more about the award here.
This year, the Society for Vascular Surgery will recognize a member in community practice who excels, leads and contributes. If you know of such a surgeon, make your nominations for the SVS Excellence in Community Service Award by Feb. 1. The first recipient will be announced at the 2019 Vascular Annual Meeting in June. Applicants must have a minimum of 20 years as a practicing vascular surgeon and a minimum of five years as an SVS member. Learn more about the award here.
AGA to FDA: We support new labeling recommendations for probiotics
In a new comment letter to FDA, AGA commends FDA’s recent draft guidance – “Policy Regarding Quantitative Labeling of Dietary Supplements Containing Live Microbials” – clarifying the expectations of probiotics manufacturers who choose to specify the amount of a live microbial component in their product in colony forming units (CFUs).
Though manufacturers are not currently required to report CFUs, AGA feels strongly that all manufacturers of probiotic supplements should voluntarily report the composition of live microbials in their products as CFUs.
However, reporting CFUs alone provides insufficient information to consumers and health care professionals who may recommend probiotic supplements to their patients. In our comment letter, AGA encourages FDA to expand what information manufacturers are required to include. In addition to the conditions already outlined in FDA’s draft guidance, AGA recommends including the conditions of storage as well as an expiration or “use by” date.
We acknowledge that researchers are evaluating other methods and units of measure besides CFUs for not only live microbials but also microbial bioactivity. However, in the absence of a widely accepted alternative, which may take several years to develop and adopt, AGA strongly encourages FDA and manufacturers to take the small step forward of using CFUs now rather than waiting for another solution to emerge.
Probiotics have been an important focus for the AGA Center for Gut Microbiome Research and Education due to the need for evidence-based guidance for health care providers and their patients. The center will continue to work to educate physicians, patients and industry on best practices to ensure safe use of probiotics.
In a new comment letter to FDA, AGA commends FDA’s recent draft guidance – “Policy Regarding Quantitative Labeling of Dietary Supplements Containing Live Microbials” – clarifying the expectations of probiotics manufacturers who choose to specify the amount of a live microbial component in their product in colony forming units (CFUs).
Though manufacturers are not currently required to report CFUs, AGA feels strongly that all manufacturers of probiotic supplements should voluntarily report the composition of live microbials in their products as CFUs.
However, reporting CFUs alone provides insufficient information to consumers and health care professionals who may recommend probiotic supplements to their patients. In our comment letter, AGA encourages FDA to expand what information manufacturers are required to include. In addition to the conditions already outlined in FDA’s draft guidance, AGA recommends including the conditions of storage as well as an expiration or “use by” date.
We acknowledge that researchers are evaluating other methods and units of measure besides CFUs for not only live microbials but also microbial bioactivity. However, in the absence of a widely accepted alternative, which may take several years to develop and adopt, AGA strongly encourages FDA and manufacturers to take the small step forward of using CFUs now rather than waiting for another solution to emerge.
Probiotics have been an important focus for the AGA Center for Gut Microbiome Research and Education due to the need for evidence-based guidance for health care providers and their patients. The center will continue to work to educate physicians, patients and industry on best practices to ensure safe use of probiotics.
In a new comment letter to FDA, AGA commends FDA’s recent draft guidance – “Policy Regarding Quantitative Labeling of Dietary Supplements Containing Live Microbials” – clarifying the expectations of probiotics manufacturers who choose to specify the amount of a live microbial component in their product in colony forming units (CFUs).
Though manufacturers are not currently required to report CFUs, AGA feels strongly that all manufacturers of probiotic supplements should voluntarily report the composition of live microbials in their products as CFUs.
However, reporting CFUs alone provides insufficient information to consumers and health care professionals who may recommend probiotic supplements to their patients. In our comment letter, AGA encourages FDA to expand what information manufacturers are required to include. In addition to the conditions already outlined in FDA’s draft guidance, AGA recommends including the conditions of storage as well as an expiration or “use by” date.
We acknowledge that researchers are evaluating other methods and units of measure besides CFUs for not only live microbials but also microbial bioactivity. However, in the absence of a widely accepted alternative, which may take several years to develop and adopt, AGA strongly encourages FDA and manufacturers to take the small step forward of using CFUs now rather than waiting for another solution to emerge.
Probiotics have been an important focus for the AGA Center for Gut Microbiome Research and Education due to the need for evidence-based guidance for health care providers and their patients. The center will continue to work to educate physicians, patients and industry on best practices to ensure safe use of probiotics.
Memorial and honorary gifts: a special tribute
Make a tribute gift to honor someone whose life has been touched by GI research or celebrate a special occasion such as a birthday while supporting the AGA Research Awards Program through the AGA Research Foundation. A tribute gift will make your loved one feel special because it honors their passion, and also help us fund research grants to talented young investigators whose work will shape the future of clinical care.
- Giving a gift to the AGA Research Foundation in memory of a loved one. A memorial gift is a meaningful way to celebrate the legacy of a family member, friend, or colleague.
- A gift today. An outright gift will help fund the AGA Research Awards Program. Your gift will assist in furthering basic digestive disease research which can ultimately advance research into all digestive diseases. The financial benefits include an income tax deduction and possible elimination of capital gains tax.
Learn more about ways to recognize and acknowledge someone by visit our website at www.gastro.org/contribute or contact Harmony Excellent at 301-272-1602 or [email protected].
Make a tribute gift to honor someone whose life has been touched by GI research or celebrate a special occasion such as a birthday while supporting the AGA Research Awards Program through the AGA Research Foundation. A tribute gift will make your loved one feel special because it honors their passion, and also help us fund research grants to talented young investigators whose work will shape the future of clinical care.
- Giving a gift to the AGA Research Foundation in memory of a loved one. A memorial gift is a meaningful way to celebrate the legacy of a family member, friend, or colleague.
- A gift today. An outright gift will help fund the AGA Research Awards Program. Your gift will assist in furthering basic digestive disease research which can ultimately advance research into all digestive diseases. The financial benefits include an income tax deduction and possible elimination of capital gains tax.
Learn more about ways to recognize and acknowledge someone by visit our website at www.gastro.org/contribute or contact Harmony Excellent at 301-272-1602 or [email protected].
Make a tribute gift to honor someone whose life has been touched by GI research or celebrate a special occasion such as a birthday while supporting the AGA Research Awards Program through the AGA Research Foundation. A tribute gift will make your loved one feel special because it honors their passion, and also help us fund research grants to talented young investigators whose work will shape the future of clinical care.
- Giving a gift to the AGA Research Foundation in memory of a loved one. A memorial gift is a meaningful way to celebrate the legacy of a family member, friend, or colleague.
- A gift today. An outright gift will help fund the AGA Research Awards Program. Your gift will assist in furthering basic digestive disease research which can ultimately advance research into all digestive diseases. The financial benefits include an income tax deduction and possible elimination of capital gains tax.
Learn more about ways to recognize and acknowledge someone by visit our website at www.gastro.org/contribute or contact Harmony Excellent at 301-272-1602 or [email protected].
Top AGA Community patient cases
about therapy and disease management options, best practices, and diagnoses.
In case you missed it, here are the most popular clinical discussions shared in the forum recently:
1. Active colitis in a patient with previous colon cancer
This popular conversation centers around next steps for a 39-year-old previously treated for a large malignant tumor with a right hemicolectomy and chemotherapy. She was referred for a chromoendoscopy, which revealed four areas of nonpolypoid abnormal mucosa with indistinct borders and abnormal dye uptake. Biopsies also revealed low-grade dysplasia and minimally active colitis.
2. IBD in remission
A 66-year-old female with a history of Crohn’s disease is currently asymptomatic and in remission, but with low Remicade trough. The debate among physicians in the forum questions the need for further action or follow-up insight. 3. Eosinophilic esophagitis and duodenitis (http://ow.ly/kja130mRoDV)
This 40-year-old patient was originally seen for food bolus. The physician prescribed proton pump inhibitors (PPI) after a scope showed typical eosinophilic esophagitis (EoE) findings. Although he had symptoms of obstruction since he was 15, this was his first upper endoscopy. Biopsies following successful scopes showed eosinophilic duodenitis and the patient had no signs of eosinophilia in the stomach.
4. Eosinophilic esophagitis and gastric sleeve
A physician noted no established absolute contraindication for a 50-year-old patient who was seen for a presleeve gastrectomy. Others contributing to this thread shared concerns for the risk for gastroesophageal reflux disease (GERD) post-surgery and committing the patient to long-term steroids.
More clinical cases and discussions are at https://community.gastro.org/discussions.
about therapy and disease management options, best practices, and diagnoses.
In case you missed it, here are the most popular clinical discussions shared in the forum recently:
1. Active colitis in a patient with previous colon cancer
This popular conversation centers around next steps for a 39-year-old previously treated for a large malignant tumor with a right hemicolectomy and chemotherapy. She was referred for a chromoendoscopy, which revealed four areas of nonpolypoid abnormal mucosa with indistinct borders and abnormal dye uptake. Biopsies also revealed low-grade dysplasia and minimally active colitis.
2. IBD in remission
A 66-year-old female with a history of Crohn’s disease is currently asymptomatic and in remission, but with low Remicade trough. The debate among physicians in the forum questions the need for further action or follow-up insight. 3. Eosinophilic esophagitis and duodenitis (http://ow.ly/kja130mRoDV)
This 40-year-old patient was originally seen for food bolus. The physician prescribed proton pump inhibitors (PPI) after a scope showed typical eosinophilic esophagitis (EoE) findings. Although he had symptoms of obstruction since he was 15, this was his first upper endoscopy. Biopsies following successful scopes showed eosinophilic duodenitis and the patient had no signs of eosinophilia in the stomach.
4. Eosinophilic esophagitis and gastric sleeve
A physician noted no established absolute contraindication for a 50-year-old patient who was seen for a presleeve gastrectomy. Others contributing to this thread shared concerns for the risk for gastroesophageal reflux disease (GERD) post-surgery and committing the patient to long-term steroids.
More clinical cases and discussions are at https://community.gastro.org/discussions.
about therapy and disease management options, best practices, and diagnoses.
In case you missed it, here are the most popular clinical discussions shared in the forum recently:
1. Active colitis in a patient with previous colon cancer
This popular conversation centers around next steps for a 39-year-old previously treated for a large malignant tumor with a right hemicolectomy and chemotherapy. She was referred for a chromoendoscopy, which revealed four areas of nonpolypoid abnormal mucosa with indistinct borders and abnormal dye uptake. Biopsies also revealed low-grade dysplasia and minimally active colitis.
2. IBD in remission
A 66-year-old female with a history of Crohn’s disease is currently asymptomatic and in remission, but with low Remicade trough. The debate among physicians in the forum questions the need for further action or follow-up insight. 3. Eosinophilic esophagitis and duodenitis (http://ow.ly/kja130mRoDV)
This 40-year-old patient was originally seen for food bolus. The physician prescribed proton pump inhibitors (PPI) after a scope showed typical eosinophilic esophagitis (EoE) findings. Although he had symptoms of obstruction since he was 15, this was his first upper endoscopy. Biopsies following successful scopes showed eosinophilic duodenitis and the patient had no signs of eosinophilia in the stomach.
4. Eosinophilic esophagitis and gastric sleeve
A physician noted no established absolute contraindication for a 50-year-old patient who was seen for a presleeve gastrectomy. Others contributing to this thread shared concerns for the risk for gastroesophageal reflux disease (GERD) post-surgery and committing the patient to long-term steroids.
More clinical cases and discussions are at https://community.gastro.org/discussions.
New editors appointed to CMGH
The next editorial team of the AGA’s basic and translational journal CMGH has been selected. Both editors are from the University of Pennsylvania Perelman School of Medicine. Dr. Kaestner is the Thomas and Evelyn Suor Butterworth Professor in Genetics. Dr. Pack is a professor of medicine and cell and developmental biology and is an attending gastroenterologist at the Hospital of the University of Pennsylvania.
CMGH debuted in 2015 with the mission of publishing impactful digestive biology research that ranges from mechanisms of normal function to pathobiology and covers a broad spectrum of themes in gastroenterology, hepatology, and pancreatology. CMGH is open access, published eight times a year, online-only and is indexed in Medline and PubMed Central. Carrying forward the tremendous success of the journal’s current editor-in-chief, Jerrold R. Turner, MD, PhD, AGAF, and his board of editors, Drs. Kaestner and Pack’s goals include advancing the impact and reputation of CMGH, ensuring the quality and fairness of the peer-review process and introducing new content that is important to the basic and translational research community.
Dr. Kaestner and Dr. Pack’s board of editors includes:
Jonathan Katz, MD
Perelman School of Medicine, University of Pennsylvania
Alison Simmons, MD, PhD
University of Oxford
Frank Tacke, MD, PhD
Rheinisch-Westfälische Technische University
In response to the appointment, Dr. Kaestner said, “We are extremely excited about the opportunity to build on the success of the current editorial team, which has already made CMGH a go-to journal for outstanding digestive disease research. Our goals will be to extend the reach of the journal and to ensure its growth as the premier publication for basic research in gastroenterology and hepatology.”
Dr. Pack added, “The remarkable success achieved by CMGH is a testament to the skill and dedication of Dr. Turner and his associate editors, Drs. Goldenring, Rescigno and Wells, as well as the tremendous growth of impactful basic research in digestive organ biology and disease. Dr. Kaestner and I look forward to maintaining the retiring editorial team’s standard of excellence as we expand the CMGH readership and its visibility in the basic research community.”
Dr. Kaestner and Dr. Pack will begin their term in July 2019.
The next editorial team of the AGA’s basic and translational journal CMGH has been selected. Both editors are from the University of Pennsylvania Perelman School of Medicine. Dr. Kaestner is the Thomas and Evelyn Suor Butterworth Professor in Genetics. Dr. Pack is a professor of medicine and cell and developmental biology and is an attending gastroenterologist at the Hospital of the University of Pennsylvania.
CMGH debuted in 2015 with the mission of publishing impactful digestive biology research that ranges from mechanisms of normal function to pathobiology and covers a broad spectrum of themes in gastroenterology, hepatology, and pancreatology. CMGH is open access, published eight times a year, online-only and is indexed in Medline and PubMed Central. Carrying forward the tremendous success of the journal’s current editor-in-chief, Jerrold R. Turner, MD, PhD, AGAF, and his board of editors, Drs. Kaestner and Pack’s goals include advancing the impact and reputation of CMGH, ensuring the quality and fairness of the peer-review process and introducing new content that is important to the basic and translational research community.
Dr. Kaestner and Dr. Pack’s board of editors includes:
Jonathan Katz, MD
Perelman School of Medicine, University of Pennsylvania
Alison Simmons, MD, PhD
University of Oxford
Frank Tacke, MD, PhD
Rheinisch-Westfälische Technische University
In response to the appointment, Dr. Kaestner said, “We are extremely excited about the opportunity to build on the success of the current editorial team, which has already made CMGH a go-to journal for outstanding digestive disease research. Our goals will be to extend the reach of the journal and to ensure its growth as the premier publication for basic research in gastroenterology and hepatology.”
Dr. Pack added, “The remarkable success achieved by CMGH is a testament to the skill and dedication of Dr. Turner and his associate editors, Drs. Goldenring, Rescigno and Wells, as well as the tremendous growth of impactful basic research in digestive organ biology and disease. Dr. Kaestner and I look forward to maintaining the retiring editorial team’s standard of excellence as we expand the CMGH readership and its visibility in the basic research community.”
Dr. Kaestner and Dr. Pack will begin their term in July 2019.
The next editorial team of the AGA’s basic and translational journal CMGH has been selected. Both editors are from the University of Pennsylvania Perelman School of Medicine. Dr. Kaestner is the Thomas and Evelyn Suor Butterworth Professor in Genetics. Dr. Pack is a professor of medicine and cell and developmental biology and is an attending gastroenterologist at the Hospital of the University of Pennsylvania.
CMGH debuted in 2015 with the mission of publishing impactful digestive biology research that ranges from mechanisms of normal function to pathobiology and covers a broad spectrum of themes in gastroenterology, hepatology, and pancreatology. CMGH is open access, published eight times a year, online-only and is indexed in Medline and PubMed Central. Carrying forward the tremendous success of the journal’s current editor-in-chief, Jerrold R. Turner, MD, PhD, AGAF, and his board of editors, Drs. Kaestner and Pack’s goals include advancing the impact and reputation of CMGH, ensuring the quality and fairness of the peer-review process and introducing new content that is important to the basic and translational research community.
Dr. Kaestner and Dr. Pack’s board of editors includes:
Jonathan Katz, MD
Perelman School of Medicine, University of Pennsylvania
Alison Simmons, MD, PhD
University of Oxford
Frank Tacke, MD, PhD
Rheinisch-Westfälische Technische University
In response to the appointment, Dr. Kaestner said, “We are extremely excited about the opportunity to build on the success of the current editorial team, which has already made CMGH a go-to journal for outstanding digestive disease research. Our goals will be to extend the reach of the journal and to ensure its growth as the premier publication for basic research in gastroenterology and hepatology.”
Dr. Pack added, “The remarkable success achieved by CMGH is a testament to the skill and dedication of Dr. Turner and his associate editors, Drs. Goldenring, Rescigno and Wells, as well as the tremendous growth of impactful basic research in digestive organ biology and disease. Dr. Kaestner and I look forward to maintaining the retiring editorial team’s standard of excellence as we expand the CMGH readership and its visibility in the basic research community.”
Dr. Kaestner and Dr. Pack will begin their term in July 2019.
A clinician’s guide to microbiome testing
The intestinal microbiota, also commonly known as the “gut microbiome” is integral to human physiology and has wide-ranging effects on the development and function of the immune system, energy metabolism and nervous system activity. There is a lot of excitement around the potential of targeting the microbiome therapeutically to promote health and to prevent or treat medical conditions. Further, as DNA sequencing technologies and computational methods continue to improve (as reviewed by Rob Knight and colleagues in a prior editorial), there is significant interest in developing microbiome-based diagnostics for clinical applications.
The industry has recognized the consumer interest in microbiome-based diagnostics as an opportunity, and a number of commercial laboratories are marketing tests directly to patients. Physicians, particularly gastroenterologists, are increasingly being asked by their patients to help interpret such test reports; in some cases, the patient may even request a physician order to purchase the tests for insurance coverage or other reasons.
Earlier this year, AGA members had a robust discussion in the AGA Community about microbiome-based tests, requirements for physician authorization, and the clinical utility (if any) of the results of such tests. below.
Limitations of microbiome sequencing. Microbiome datasets have the same limitations as any other sample-dependent dataset. First and foremost, a single stool sample will tell you something about a person’s microbiome profile only at the time and location that the sample was collected. How the sample was collected and how it was stored may significantly impact the analysis. The analysis generally provides an overview of bacterial families and genera, but little information about the viruses, protozoa and fungi. Furthermore, stool analysis may not reflect well the microbiome composition at the mucosal surface in the intestine. As a result, a single analysis of an individual stool sample merely provides a snapshot of the fecal microbiome that is incomplete and extremely limited in what we can learn from it.
“Good” vs. “bad.” The reports resulting from microbiome-based tests often describe the patient’s microbiome profile in terms of how much “good” and “bad” bacteria are present. This kind of a classification framework represents a naïve and cartoonish view of the microbial world. Instead, it is important to appreciate microbial communities as functional networks, and that their functionality cannot be defined as a mere summation of individual microorganisms. Microbes, just like people, vary their behavior in accordance with the context that may be provided by the activity of other microbes and the host. Whether a particular species or strain is helpful or harmful depends on what other bacteria are present, their density, how they interact with each other (e.g., are they mutually beneficial or competitive?), and factors from the human host such as their diet or immune system activity. For example, Clostridioides difficile is a potential pathogen, yet it also naturally exists in the intestines of many people as a nonharmful, commensal species. Its pathogenic potential depends on the state of the other intestinal microbes and host factors, such as presence of anti-C. difficile toxin antibodies.
Importantly, microbiome tests, which generally provide only a low-resolution microbial community overview, are not designed for pathogen identification. That is best done with targeted diagnostics. Even then, as well illustrated by the C. difficileexample, diagnosis of an infection cannot be made on the basis of laboratory testing alone and requires clinical information.
Taxonomy vs. function. Current technology allows a fairly inexpensive characterization of most bacterial taxa (at family and genus levels). However, taxonomy is not easily translated into functional information. Different taxa of microbes may be able to execute the same chemical transformations. In contrast, functional information depends on the genes present and how much are these genes expressed. However, obtaining this kind of information is much more resource intensive. Measurements of metabolites may also provide very valuable functional information, but proper sample collection for metabolomics is much more difficult.
Interindividual variability. The consistent lesson we’ve learned from the microbiome literature is that there is not a single “healthy” microbiome profile. We have not identified a particular microbiome profile that is predictive of a particular disease, though many researchers are working to develop microbiome-based indices for diseases such as inflammatory bowel disease or obesity. Crowd-sourced studies such as the American Gut Project are working to expand and diversify microbiome datasets so that we can better understand the variability and begin to identify reproducible microbiome signatures. The microbiome data is extremely multidimensional and complex. Therefore, developing predictive patterns will likely require analyses of millions of samples linked to highly granular clinical metadata. Microbiome-based tests have potential to transform clinical care and become incorporated into the personalized medicine paradigm. However, we are at the very beginning of understanding what one’s microbiome profile means for their susceptibility to or progression of disease. As patients approach their health care providers with requests to order commercial microbiome-based tests or to help interpret a report, it is important to set the expectation that these tests are not well suited for diagnoses of infectious diseases or validated in specific diagnoses of any diseases. There are far more unknowns than knowns regarding the role of the microbiome and human health.
For those interested in learning more on this topic, I will be discussing it at the 2019 Gut Microbiota for Health World Summit with my colleague Diane Hoffmann, JD, MS, from the University of Maryland School of Law. The AGA Center for Gut Microbiome Research and Education’s scientific advisory board, on which Diane and I both serve, has also recognized the need for additional guidance. I would encourage my gastroenterology colleagues to continue sharing their experiences with microbiome-based tests through the AGA Community platform.
Recommended reading
- • Staley C, Kaiser T, Khoruts A. Clinician guide to microbiome testing. Dig Dis Sci. 2018 Sep 28. doi: 10.1007/s10620-018-5299-6.
- • Allaband C, McDonald D, Vazquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, et al. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol 2018. doi: 10.1016/j.cgh.2018.09.017. • Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science 2012. doi: 10.1126/science.1224203. Epub 2012 Jun 6.
Dr. Khoruts, of the University of Minnesota, is a member of the AGA Center for Gut Microbiome Research & Education scientific advisory board.
The intestinal microbiota, also commonly known as the “gut microbiome” is integral to human physiology and has wide-ranging effects on the development and function of the immune system, energy metabolism and nervous system activity. There is a lot of excitement around the potential of targeting the microbiome therapeutically to promote health and to prevent or treat medical conditions. Further, as DNA sequencing technologies and computational methods continue to improve (as reviewed by Rob Knight and colleagues in a prior editorial), there is significant interest in developing microbiome-based diagnostics for clinical applications.
The industry has recognized the consumer interest in microbiome-based diagnostics as an opportunity, and a number of commercial laboratories are marketing tests directly to patients. Physicians, particularly gastroenterologists, are increasingly being asked by their patients to help interpret such test reports; in some cases, the patient may even request a physician order to purchase the tests for insurance coverage or other reasons.
Earlier this year, AGA members had a robust discussion in the AGA Community about microbiome-based tests, requirements for physician authorization, and the clinical utility (if any) of the results of such tests. below.
Limitations of microbiome sequencing. Microbiome datasets have the same limitations as any other sample-dependent dataset. First and foremost, a single stool sample will tell you something about a person’s microbiome profile only at the time and location that the sample was collected. How the sample was collected and how it was stored may significantly impact the analysis. The analysis generally provides an overview of bacterial families and genera, but little information about the viruses, protozoa and fungi. Furthermore, stool analysis may not reflect well the microbiome composition at the mucosal surface in the intestine. As a result, a single analysis of an individual stool sample merely provides a snapshot of the fecal microbiome that is incomplete and extremely limited in what we can learn from it.
“Good” vs. “bad.” The reports resulting from microbiome-based tests often describe the patient’s microbiome profile in terms of how much “good” and “bad” bacteria are present. This kind of a classification framework represents a naïve and cartoonish view of the microbial world. Instead, it is important to appreciate microbial communities as functional networks, and that their functionality cannot be defined as a mere summation of individual microorganisms. Microbes, just like people, vary their behavior in accordance with the context that may be provided by the activity of other microbes and the host. Whether a particular species or strain is helpful or harmful depends on what other bacteria are present, their density, how they interact with each other (e.g., are they mutually beneficial or competitive?), and factors from the human host such as their diet or immune system activity. For example, Clostridioides difficile is a potential pathogen, yet it also naturally exists in the intestines of many people as a nonharmful, commensal species. Its pathogenic potential depends on the state of the other intestinal microbes and host factors, such as presence of anti-C. difficile toxin antibodies.
Importantly, microbiome tests, which generally provide only a low-resolution microbial community overview, are not designed for pathogen identification. That is best done with targeted diagnostics. Even then, as well illustrated by the C. difficileexample, diagnosis of an infection cannot be made on the basis of laboratory testing alone and requires clinical information.
Taxonomy vs. function. Current technology allows a fairly inexpensive characterization of most bacterial taxa (at family and genus levels). However, taxonomy is not easily translated into functional information. Different taxa of microbes may be able to execute the same chemical transformations. In contrast, functional information depends on the genes present and how much are these genes expressed. However, obtaining this kind of information is much more resource intensive. Measurements of metabolites may also provide very valuable functional information, but proper sample collection for metabolomics is much more difficult.
Interindividual variability. The consistent lesson we’ve learned from the microbiome literature is that there is not a single “healthy” microbiome profile. We have not identified a particular microbiome profile that is predictive of a particular disease, though many researchers are working to develop microbiome-based indices for diseases such as inflammatory bowel disease or obesity. Crowd-sourced studies such as the American Gut Project are working to expand and diversify microbiome datasets so that we can better understand the variability and begin to identify reproducible microbiome signatures. The microbiome data is extremely multidimensional and complex. Therefore, developing predictive patterns will likely require analyses of millions of samples linked to highly granular clinical metadata. Microbiome-based tests have potential to transform clinical care and become incorporated into the personalized medicine paradigm. However, we are at the very beginning of understanding what one’s microbiome profile means for their susceptibility to or progression of disease. As patients approach their health care providers with requests to order commercial microbiome-based tests or to help interpret a report, it is important to set the expectation that these tests are not well suited for diagnoses of infectious diseases or validated in specific diagnoses of any diseases. There are far more unknowns than knowns regarding the role of the microbiome and human health.
For those interested in learning more on this topic, I will be discussing it at the 2019 Gut Microbiota for Health World Summit with my colleague Diane Hoffmann, JD, MS, from the University of Maryland School of Law. The AGA Center for Gut Microbiome Research and Education’s scientific advisory board, on which Diane and I both serve, has also recognized the need for additional guidance. I would encourage my gastroenterology colleagues to continue sharing their experiences with microbiome-based tests through the AGA Community platform.
Recommended reading
- • Staley C, Kaiser T, Khoruts A. Clinician guide to microbiome testing. Dig Dis Sci. 2018 Sep 28. doi: 10.1007/s10620-018-5299-6.
- • Allaband C, McDonald D, Vazquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, et al. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol 2018. doi: 10.1016/j.cgh.2018.09.017. • Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science 2012. doi: 10.1126/science.1224203. Epub 2012 Jun 6.
Dr. Khoruts, of the University of Minnesota, is a member of the AGA Center for Gut Microbiome Research & Education scientific advisory board.
The intestinal microbiota, also commonly known as the “gut microbiome” is integral to human physiology and has wide-ranging effects on the development and function of the immune system, energy metabolism and nervous system activity. There is a lot of excitement around the potential of targeting the microbiome therapeutically to promote health and to prevent or treat medical conditions. Further, as DNA sequencing technologies and computational methods continue to improve (as reviewed by Rob Knight and colleagues in a prior editorial), there is significant interest in developing microbiome-based diagnostics for clinical applications.
The industry has recognized the consumer interest in microbiome-based diagnostics as an opportunity, and a number of commercial laboratories are marketing tests directly to patients. Physicians, particularly gastroenterologists, are increasingly being asked by their patients to help interpret such test reports; in some cases, the patient may even request a physician order to purchase the tests for insurance coverage or other reasons.
Earlier this year, AGA members had a robust discussion in the AGA Community about microbiome-based tests, requirements for physician authorization, and the clinical utility (if any) of the results of such tests. below.
Limitations of microbiome sequencing. Microbiome datasets have the same limitations as any other sample-dependent dataset. First and foremost, a single stool sample will tell you something about a person’s microbiome profile only at the time and location that the sample was collected. How the sample was collected and how it was stored may significantly impact the analysis. The analysis generally provides an overview of bacterial families and genera, but little information about the viruses, protozoa and fungi. Furthermore, stool analysis may not reflect well the microbiome composition at the mucosal surface in the intestine. As a result, a single analysis of an individual stool sample merely provides a snapshot of the fecal microbiome that is incomplete and extremely limited in what we can learn from it.
“Good” vs. “bad.” The reports resulting from microbiome-based tests often describe the patient’s microbiome profile in terms of how much “good” and “bad” bacteria are present. This kind of a classification framework represents a naïve and cartoonish view of the microbial world. Instead, it is important to appreciate microbial communities as functional networks, and that their functionality cannot be defined as a mere summation of individual microorganisms. Microbes, just like people, vary their behavior in accordance with the context that may be provided by the activity of other microbes and the host. Whether a particular species or strain is helpful or harmful depends on what other bacteria are present, their density, how they interact with each other (e.g., are they mutually beneficial or competitive?), and factors from the human host such as their diet or immune system activity. For example, Clostridioides difficile is a potential pathogen, yet it also naturally exists in the intestines of many people as a nonharmful, commensal species. Its pathogenic potential depends on the state of the other intestinal microbes and host factors, such as presence of anti-C. difficile toxin antibodies.
Importantly, microbiome tests, which generally provide only a low-resolution microbial community overview, are not designed for pathogen identification. That is best done with targeted diagnostics. Even then, as well illustrated by the C. difficileexample, diagnosis of an infection cannot be made on the basis of laboratory testing alone and requires clinical information.
Taxonomy vs. function. Current technology allows a fairly inexpensive characterization of most bacterial taxa (at family and genus levels). However, taxonomy is not easily translated into functional information. Different taxa of microbes may be able to execute the same chemical transformations. In contrast, functional information depends on the genes present and how much are these genes expressed. However, obtaining this kind of information is much more resource intensive. Measurements of metabolites may also provide very valuable functional information, but proper sample collection for metabolomics is much more difficult.
Interindividual variability. The consistent lesson we’ve learned from the microbiome literature is that there is not a single “healthy” microbiome profile. We have not identified a particular microbiome profile that is predictive of a particular disease, though many researchers are working to develop microbiome-based indices for diseases such as inflammatory bowel disease or obesity. Crowd-sourced studies such as the American Gut Project are working to expand and diversify microbiome datasets so that we can better understand the variability and begin to identify reproducible microbiome signatures. The microbiome data is extremely multidimensional and complex. Therefore, developing predictive patterns will likely require analyses of millions of samples linked to highly granular clinical metadata. Microbiome-based tests have potential to transform clinical care and become incorporated into the personalized medicine paradigm. However, we are at the very beginning of understanding what one’s microbiome profile means for their susceptibility to or progression of disease. As patients approach their health care providers with requests to order commercial microbiome-based tests or to help interpret a report, it is important to set the expectation that these tests are not well suited for diagnoses of infectious diseases or validated in specific diagnoses of any diseases. There are far more unknowns than knowns regarding the role of the microbiome and human health.
For those interested in learning more on this topic, I will be discussing it at the 2019 Gut Microbiota for Health World Summit with my colleague Diane Hoffmann, JD, MS, from the University of Maryland School of Law. The AGA Center for Gut Microbiome Research and Education’s scientific advisory board, on which Diane and I both serve, has also recognized the need for additional guidance. I would encourage my gastroenterology colleagues to continue sharing their experiences with microbiome-based tests through the AGA Community platform.
Recommended reading
- • Staley C, Kaiser T, Khoruts A. Clinician guide to microbiome testing. Dig Dis Sci. 2018 Sep 28. doi: 10.1007/s10620-018-5299-6.
- • Allaband C, McDonald D, Vazquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, et al. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol 2018. doi: 10.1016/j.cgh.2018.09.017. • Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science 2012. doi: 10.1126/science.1224203. Epub 2012 Jun 6.
Dr. Khoruts, of the University of Minnesota, is a member of the AGA Center for Gut Microbiome Research & Education scientific advisory board.
Rising microbiome investigator: Lea Ann Chen, MD
We spoke with Dr. Chen, assistant professor of medicine at New York University and the recipient of the AGA Research Foundation’s 2016 Research Scholar Award, to learn about her work on the gut microbiome and inflammatory bowel disease (IBD).
How would you sum up your research in one sentence?
I study longitudinal changes of the gut microbiome as it relates to gastrointestinal illnesses, particularly IBD.
What impact do you hope your research will have on patients?
I hope that my research will provide greater insights into the role of gut microbes in disease pathogenesis and activity to ultimately inform the development of new diagnostics and treatments.
What inspired you to focus your research career on the gut microbiome?
I’ve long been fascinated by ecological systems and host-microbe interactions. As technologies to study the gut microbiome became more readily available, I was eager, and somewhat relieved, to be able to combine my research interests with my clinical interest in gastroenterology.
What recent publication from your lab best represents your work, if anyone wants to learn more?
In this study, we show that gut bacterial disturbances are resolved after fecal transplantation in children without IBD but are only transiently resolved in those with IBD.
Hourigan S.*, Chen L.A.*, Grigoryan Z., et al. Microbiome changes associated with sustained eradication of Clostridium difficile after fecal microbiota transplantation in children with and without inflammatory bowel disease. Aliment Pharmacol Ther. 2015;42:741-52.
You’re involved with several AGA initiatives including the Future Leaders Program and the FMT National Registry. How has being an AGA member impacted your career?
AGA has provided key mentorship and training opportunities that have been instrumental in my career development. It has further helped me discover a diverse community of clinicians and scientists who are amazing role models, resources and colleagues. I really had no inkling what was in store when I first joined AGA as a trainee, but I feel very lucky that I did and am grateful for how AGA membership has really enriched my life as a gastroenterologist.
We spoke with Dr. Chen, assistant professor of medicine at New York University and the recipient of the AGA Research Foundation’s 2016 Research Scholar Award, to learn about her work on the gut microbiome and inflammatory bowel disease (IBD).
How would you sum up your research in one sentence?
I study longitudinal changes of the gut microbiome as it relates to gastrointestinal illnesses, particularly IBD.
What impact do you hope your research will have on patients?
I hope that my research will provide greater insights into the role of gut microbes in disease pathogenesis and activity to ultimately inform the development of new diagnostics and treatments.
What inspired you to focus your research career on the gut microbiome?
I’ve long been fascinated by ecological systems and host-microbe interactions. As technologies to study the gut microbiome became more readily available, I was eager, and somewhat relieved, to be able to combine my research interests with my clinical interest in gastroenterology.
What recent publication from your lab best represents your work, if anyone wants to learn more?
In this study, we show that gut bacterial disturbances are resolved after fecal transplantation in children without IBD but are only transiently resolved in those with IBD.
Hourigan S.*, Chen L.A.*, Grigoryan Z., et al. Microbiome changes associated with sustained eradication of Clostridium difficile after fecal microbiota transplantation in children with and without inflammatory bowel disease. Aliment Pharmacol Ther. 2015;42:741-52.
You’re involved with several AGA initiatives including the Future Leaders Program and the FMT National Registry. How has being an AGA member impacted your career?
AGA has provided key mentorship and training opportunities that have been instrumental in my career development. It has further helped me discover a diverse community of clinicians and scientists who are amazing role models, resources and colleagues. I really had no inkling what was in store when I first joined AGA as a trainee, but I feel very lucky that I did and am grateful for how AGA membership has really enriched my life as a gastroenterologist.
We spoke with Dr. Chen, assistant professor of medicine at New York University and the recipient of the AGA Research Foundation’s 2016 Research Scholar Award, to learn about her work on the gut microbiome and inflammatory bowel disease (IBD).
How would you sum up your research in one sentence?
I study longitudinal changes of the gut microbiome as it relates to gastrointestinal illnesses, particularly IBD.
What impact do you hope your research will have on patients?
I hope that my research will provide greater insights into the role of gut microbes in disease pathogenesis and activity to ultimately inform the development of new diagnostics and treatments.
What inspired you to focus your research career on the gut microbiome?
I’ve long been fascinated by ecological systems and host-microbe interactions. As technologies to study the gut microbiome became more readily available, I was eager, and somewhat relieved, to be able to combine my research interests with my clinical interest in gastroenterology.
What recent publication from your lab best represents your work, if anyone wants to learn more?
In this study, we show that gut bacterial disturbances are resolved after fecal transplantation in children without IBD but are only transiently resolved in those with IBD.
Hourigan S.*, Chen L.A.*, Grigoryan Z., et al. Microbiome changes associated with sustained eradication of Clostridium difficile after fecal microbiota transplantation in children with and without inflammatory bowel disease. Aliment Pharmacol Ther. 2015;42:741-52.
You’re involved with several AGA initiatives including the Future Leaders Program and the FMT National Registry. How has being an AGA member impacted your career?
AGA has provided key mentorship and training opportunities that have been instrumental in my career development. It has further helped me discover a diverse community of clinicians and scientists who are amazing role models, resources and colleagues. I really had no inkling what was in store when I first joined AGA as a trainee, but I feel very lucky that I did and am grateful for how AGA membership has really enriched my life as a gastroenterologist.
Apply for a VRIC Travel Scholarship
The Vascular Research Initiatives Conference emphasizes emerging vascular science and encourages interactive participation of attendees, including trainees who are aspiring academic vascular surgeons. The SVS Foundation offers the Vascular Research Initiatives Conference Trainee Travel Scholarship for trainees to attend the conference. The trainee authors of top-scoring abstracts will be considered for the award, which includes complimentary registration to VRIC as well as the American Heart Association's Vascular Discover Scientific Sessions, plus $1,000 for conference travel. Applications are accepted until Jan 15, 2019.
The Vascular Research Initiatives Conference emphasizes emerging vascular science and encourages interactive participation of attendees, including trainees who are aspiring academic vascular surgeons. The SVS Foundation offers the Vascular Research Initiatives Conference Trainee Travel Scholarship for trainees to attend the conference. The trainee authors of top-scoring abstracts will be considered for the award, which includes complimentary registration to VRIC as well as the American Heart Association's Vascular Discover Scientific Sessions, plus $1,000 for conference travel. Applications are accepted until Jan 15, 2019.
The Vascular Research Initiatives Conference emphasizes emerging vascular science and encourages interactive participation of attendees, including trainees who are aspiring academic vascular surgeons. The SVS Foundation offers the Vascular Research Initiatives Conference Trainee Travel Scholarship for trainees to attend the conference. The trainee authors of top-scoring abstracts will be considered for the award, which includes complimentary registration to VRIC as well as the American Heart Association's Vascular Discover Scientific Sessions, plus $1,000 for conference travel. Applications are accepted until Jan 15, 2019.