Examples of Client Studies

Differding MK, Benjamin-Neelon SE, Hoyo C, Østbye T & Mueller NT. Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life. BMC Microbiology, 56(2020).

Differding MK, Benjamin-Neelon SE, et al. Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome. Annals of Clinical Microbiology and Antimicrobials, 18(2019)

Gudi R, Suber J, Brown R, Johnson BM, Vasu C. Pretreatment with yeast derived complex dietary-polysaccharide leads to suppressed gut inflammation, altered microbiota composition and increased immune regulatory short-chain fatty acid production in C57BL/6 mice. doi: https://doi.org/10.1101/719112

Sugden S, St. Clair CC, Stein LY. Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota. Microbial Ecology (2020).

We know from humans that the microbiome varies along the length of the intestinal tract; however, little knowledge of the intestinal microbiota is available for wild animals. This study profiles the microbiota at seven sites along the coyote intestinal tract and shows that, aside from broad differences between the small and large intestine, the gut microbiota is more distinct between individuals than it is between intestinal sites.

Peng Y, Tan Q, Afhami S, Deehan EC, et al. The Gut Microbiota Profile in Children with Prader–Willi Syndrome. Genes 202, 11(8) 904.

This study characterized the gut bacterial and fungal communities of children with Prader-Willi syndrome, which were different from that of healthy controls, and showed that microbial composition in affected children was associated with hyperphagia symptom severity.  

Allushi B, Bagavant H, Papinska J, Deshmukh US. Hyperglycemia and Salivary Gland Dysfunction in the Non-obese Diabetic Mouse: Caveats for Preclinical Studies in Sjögren’s Syndrome. Scientific Reports, 17969 (2019).

Estrela S, Sanchez-Gorostiaga A, Vila JCC, Sanchez A. Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments. doi: https://doi.org/10.1101/2020.08.06.239897

Messman RD, Contreras-Correa ZE, Paz HA, Perry G, Lemley CO. Vaginal bacterial community composition and concentrations of estradiol at the time of artificial insemination in Brangus heifers. Journal of Animal Science (2020), 98; 6.

In Brangus heifers, the overall composition of the vaginal microbiota was not altered by pregnancy status or endogenous estradiol concentrations at timed artificial insemination. However, there were species level differences that could have implications in reproductive performance and warrant further investigation.

Marianne Collard, Nataleigh Austin, Ann Tallant, Patricia Gallagher Muscadine Grape Extract Reduces Lung and Liver Metastasis in Mice with Triple Negative Breast Cancer in Association with Changes in the Gut Microbiome (P05-017-19). Current Developments in Nutrition 2019, 3; 1.

Charania R, Wade BE, McNair NN, Mead JR. Changes in the Microbiome of Cryptosporidium-Infected Mice Correlate to Differences in Susceptibility and Infection Levels. Microorganisms 2020, 8(6), 879. 

This study examined changes in bacterial flora following antibiotic treatment to determine how cryptosporidial infections and gut integrity were affected by alterations in the microbiome. In particular, cloxacillin treatment of mice increased susceptibility, induced changes in the microbiota and decreases in some short chain fatty acids, suggesting that depletion of certain bacterial populations may change the microbiota dynamics and subsequently metabolites present allowing for greater susceptibility. 

Barelli L, Waller AS, Behie SW, Bidochka MJ. Plant Microbiome Analysis after Metarhizium Amendment Reveals Increases in Abundance of Plant Growth-Promoting Organisms and Maintenance of Disease-Suppressive Soil. PLoS ONE (2020) 15(4): e0231150.

Schmidt EKA, Torres-Espin A, Raposo PJF, Madsen KL, Kigerl KA, Popovich PG, et al. Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats. PLoS ONE. 2020;15(1):e0226128. doi:10.1371/journal.pone.0226128

Spinal cord injury often co-occurs with depression and anxiety. This work investigated whether the latter could be prevented by targeting the gut microbiota. Researchers found that spinal cord injury induced gut microbiota dysbiosis and increased anxiety-like behaviors in rats; but fecal microbiota transplantation in the rats prevented both the dysbiosis and anxiety-like behaviors.

Boomana M, Forster I, Vederas J, Groman D, Jones S. Soybean meal-induced enteritis in Atlantic salmon (Salmo salar) and Chinook salmon (Oncorhynchus tshawytscha) but not in pink salmon (O. gorbuscha). Aquaculture. 2018; 483: 238-243.

This study compared intestinal pathology and the microbiome of different salmon fed a diet comprising 20% soybean meal; researchers found that mucosal enteritis varied among salmon species but the diet had no influence on microbiome diversity or composition.

Dimitriu PA, Iker B, Malik K, Leung H, Mohn WW, Hillebrand, GG. New insights into the intrinsic and extrinsic factors that shape the human skin microbiome. mBio. 2019.

This epidemiological study was the largest human skin microbiome survey ever published; it included 495 individuals between the ages of 9 and 78, with over 2500 skin swab samples from four skin sites and the mouth. Between 12 and 20 percent of the bacterial microbiome variability was explained by demographic, physiologic, and lifestyle factors. Also, specific taxa on the skin were associated with chronological age.

Nielsen G, Hatam I, Abuan K, et al. Semi-passive in-situ pilot scale bioreactor successfully removed sulfate and metals from mine impacted water under subarctic climatic conditions. Water Res. 2018; 140: 268-279.

Researchers in this study tested whether sulfate reducing bacteria in subarctic mine environments can be enriched with a carbon source to remove sulfate and metals in a semi passive pilot scale bioreactor. Molasses was added to anaerobic bioreactors to mimic in situ conditions and microbial analysis confirmed the sulfate reducing bacteria were enriched and the population remained stable over 14 months. Removal efficiency of Zn and Cd varied from 20.9% in winter to 89.3% in summer and 39% in winter to 90.5% in summer, respectively.’

Patankar J, Wong C, Morampudi V, et al. Genetic ablation of Cyp8b1 preserves host metabolic function by repressing steatohepatitis and altering gut microbiota composition. Am J Physiol Endocrinol Metab. 2018; 314: E418-E432.

This study found, in Cyp8b1-/- mice, that altered bile acid composition maintains metabolic and respiratory function by repressing hepatic de novo lipogenesis and driving beneficial changes in gut microbiota.

Subedi G, Taylor J, Hatam I, Baldwin S. Simultaneous selenate reduction and denitrification by a consortium of enriched mine site bacteria. Chemosphere. 2017; 183: 536-545.

In this study, researchers report on an enrichment of a bacterial assemblage capable of denitrification and selenate reduction in natural marsh sediment impacted by a mine. Genomic analysis of the bacteria uncovered open reading frames homologous to selenate reductase subunits. The results indicate that native mine site bacteria may be used to remove selenate and nitrate from wastewater.

Tremblay S, Côté N, Grenier G, et al. Ileal antimicrobial peptide expression is dysregulated in old age. Immun Ageing. 2017; 14: 19.

In this study, which aimed to uncover the mechanisms underlying geriatric gastrointestinal dysfunction, researchers found changes in antimicrobial peptide gene expression as well as histological damage of the ileal epithelium and slight differences in gut microbiota composition in aged mice.

Vonaesch P, Morien E, Andrianonimiadana L, et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. PNAS. 2018; 115(36): E8489-E8498.

Vonaesch P, Randremanana R, Gody J-C, et al. Identifying the etiology and pathophysiology underlying stunting and environmental enteropathy: study protocol of the AFRIBIOTA project. BMC Pediatrics. 2018; 18: 236.

Stunting, a condition that affects roughly 25% of the world’s children leads to long-term negative health outcomes. The condition has long been linked to poor nutrition and recurrent intestinal infections. Recently a condition called pediatric environmental enteropathy (PEE) characterized by chronic inflammation of the small intestine has been suggested as an underlying cause of stunting and its resistance to treatment. To address the lack of data describing intestinal microbiota associated with stunting and PEE, the AFRIOBIOTA project (see 2 publications above) collected duodenal, gastric and fecal samples from stunted children in sub-Saharan Africa, and used both sequencing and culture methods to characterize the microbiota. The investigation found that many of the enrolled children had a small intestinal overgrowth of bacteria normally found in the oropharyngeal cavity. Escherichia coli, Shigella sp. and Campylobacter sp. were also found to be more prevalent while known butyrate producing species Clostridia were reduced. The data points to evidence for microbiome “decompartmentalization” in the small intestine and an association with stunting and the chronic inflammation characteristic of PEE. The observed overrepresentations of oral bacteria in the fecal samples could lead to non-invasive diagnostic markers.

Yang I, Knight AK, Dunlop AL, Corwin EJ. Characterizing the Subgingival Microbiome of Pregnant African American Women. Journal of Obstetric, Gynecologic & Neonatal Nursing. 2019; 48(2), 140–152.

This pilot study examined how the oral microbiome in pregnant women relates to adverse pregnancy outcomes, including preterm birth. The authors examined the subgingival microbiota of African American women (n=34) in their third trimester of pregnancy and classified each woman as having a healthy gingiva or gingivitis. No differences in microbiota diversity were observed between those with gingivitis and those without, but specific bacterial taxa differed in the two groups. Neither the subgingival microbiota nor oral inflammation was linked with preterm birth.

Alhasan MM, Cait AM, Heimesaat MM, et al. Antibiotic use during pregnancy increases offspring asthma severity in a dose-dependent manner. Allergy. 2020;00:1–12. https://doi.org/10.1111/all.14234

This study using mice shows that treatment of pregnant mothers with antibiotics changes the gut microbiome of their offspring and predisposes the offspring to more severe asthma.

Brett Finlay – Co-Founder and Scientific Advisor

Our co-founding scientists and our technical team are active contributors to the scientific literature on the microbiome. Below, we highlight some of the most important recent publications.

Arrieta MC, Arévalo A, Stiemsma L, et al. Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting. J Allergy Clin Immunol. 2018.

Cait A, Hughes M, Antignano F, et al. Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids. Mucosal Immunol. 2018; 11: 785-795.

Costea P, Zeller G, Sunagawa S, et al. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol. 2017; 35: 1069-1076.

Arrieta M, Stiemsma L, Dimitriu P, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015; 7: 307ra152.

Brown E, Wlodarska M, Willing B, et al. Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model. Nat Commun. 2015; 6: 7806.

Huus, K.E., Rodriguez-Pozo, A., Kapel, N. et al. Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota studyMicrobiome 8, 113 (2020).

Cirstea, M.S., Yu, A.C., Golz, E., Sundvick, K., Kliger, D., Radisavljevic, N., Foulger, L.H., Mackenzie, M., Huan, T., Finlay, B.B. and Appel‐Cresswell, S. (2020), Microbiota Composition and Metabolism Are Associated With Gut Function in Parkinson’s Disease. Mov Disord, 35: 1208-1217

David M Patrick, Hind Sbihi, Darlene L Y Dai, Abdullah Al Mamun, Drona Rasali, Caren Rose, Fawziah Marra, Rozlyn C T Boutin, Charisse Petersen, Leah T Stiemsma, Geoffrey L Winsor, Fiona S L Brinkman, Anita L Kozyrskyj, Meghan B Azad, Allan B Becker, Piush J Mandhane, Theo J Moraes, Malcolm R Sears, Padmaja Subbarao, B Brett Finlay, Stuart E Turvey, Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies, The Lancet Respiratory Medicine, 2020.

Finlay BB, Goldszmid R, Honda K, Trinchieri G, Wargo J, Zitvogel L. Can we harness the microbiota to enhance the efficacy of cancer immunotherapy? Nature Reviews Immunology. 2020

Search PubMed for current results.

Bill Mohn – Co-Founder and Scientific Advisor

Alhasan MM, Cait AM, Heimesaat MM, Blaut M, Klopfleisch R, Mohn, WW, et al. Antibiotic use during pregnancy increases offspring asthma severity in a dose-dependent manner. Allergy, 2020;75:1979-1990.

This study using mice shows that treatment of pregnant mothers with antibiotics changes the gut microbiome of their offspring and predisposes the offspring to more severe asthma.

Amenyogbe NM, Adu-Gyasi D, Enuameh Y, Asante KP, Konadu DG, Seyram K, Mohn WW et al.

Bacterial and Fungal Gut Community Dynamics Over the First Five Years of Life in Predominantly Rural Communities in Ghana DOI:10.21203/rs.3.rs-78160/v1

Cardenas E, Orellana L, Konstantinidis K, Mohn W. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. Sci Rep. 2018; 8: 3142.

Holert J, Cardenas E, Bergstrand L, et al. Metagenomes reveal global distribution of bacterial steroid catabolism in natural, engineered and host environments. mBio. 2018; 9: e02345-17.

Cait A, Hughes M, Antignano F, et al. Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids. Mucosal Immunol. 2018; 11: 785-795.

Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J. 2018 (in press).

Cait A, Cardenas E, Dimitriu P, Amenyogbe N, Dai D, Cait J, Sbihi H, Stiemsma L, Subbarao P, Mandhane PJ, Becker AB, Moraes TJ, Sears MR, Lefebvre DL, Azad MB, Kollmann T, Turvey SE, Mohn WW. Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization. J Allergy Clin Immunol. 2019.

Levy-Booth DJ, Fetherolf MM, Stewart GR, Liu J, Eltis LD, Mohn WW. Catabolism of Alkylphenols in Rhodococcus via a Meta-Cleavage Pathway Associated With Genomic Islands. Front Microbiol. 2019

Holert J, Brown K, Hashimi A, Eltis LD, Mohn WW. Steryl Ester Formation and Accumulation in Steroid-Degrading Bacteria. Appl Environ Microbiol. 2020

Alhasan MM, Cait AM, Heimesaat MM, et al. Antibiotic use during pregnancy increases offspring asthma severity in a dose-dependent manner. Allergy. 2020

Search PubMed for current results