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1. Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome.

Author

Labus, Jennifer S, Hollister, Emily B, Jacobs, Jonathan, Kirbach, Kyleigh, Oezguen, Numan, Gupta, Arpana, Acosta, Jonathan, Luna, Ruth Ann, Aagaard, Kjersti, Versalovic, James, Savidge, Tor, Hsiao, Elaine, Tillisch, Kirsten, and Mayer, Emeran A

Subjects
Brain, Feces, Humans, Bacteria, Irritable Bowel Syndrome, DNA, Bacterial, DNA, Ribosomal, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Phylogeny, Adult, Female, Male, Young Adult, Gastrointestinal Microbiome, Bacteroidetes, Brain-gut-microbiome axis, Firmicutes, Irritable bowel syndrome, Metagenome, Ecology, Microbiology, Medical Microbiology
Abstract

BackgroundPreclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS.MethodsBehavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs). 16S ribosomal RNA (rRNA) gene sequencing was used to profile stool microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity. The metagenomic content of samples was inferred from 16S rRNA gene sequence data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). T1-weighted brain images were acquired on a Siemens Allegra 3T scanner, and morphological measures were computed for 165 brain regions.ResultsUsing unweighted Unifrac distances with hierarchical clustering on microbial data, samples were clustered into two IBS subgroups within the IBS population (IBS1 (n = 13) and HC-like IBS (n = 16)) and HCs (n = 23) (AUROC = 0.96, sensitivity 0.95, specificity 0.67). A Random Forest classifier provided further support for the differentiation of IBS1 and HC groups. Microbes belonging to the genera Faecalibacterium, Blautia, and Bacteroides contributed to this subclassification. Clinical features distinguishing the groups included a history of early life trauma and duration of symptoms (greater in IBS1), but not self-reported bowel habits, anxiety, depression, or medication use. Gut microbial composition correlated with structural measures of brain regions including sensory- and salience-related regions, and with a history of early life trauma.ConclusionsThe results confirm previous reports of gut microbiome-based IBS subgroups and identify for the first time brain structural alterations associated with these subgroups. They provide preliminary evidence for the involvement of specific microbes and their predicted metabolites in these correlations.

Published
2017

15. Fecal Microbiota Transplantation Commonly Failed in Children With Co-Morbidities

Author

Kellermayer, Richard, primary, Wu, Qinglong, additional, Nagy-Szakal, Dorottya, additional, Queliza, Karen, additional, Ihekweazu, Faith D., additional, Bocchini, Claire E., additional, Magee, Abria R., additional, Oezguen, Numan, additional, Spinler, Jennifer K., additional, Hollister, Emily B., additional, Shulman, Robert J., additional, Versalovic, James, additional, Luna, Ruth Ann, additional, and Savidge, Tor C., additional

Published
2021
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17. Probiotic VSL#3 Treatment Reduces Colonic Permeability and Abdominal Pain Symptoms in Patients With Irritable Bowel Syndrome

Author

Boonma, Prapaporn, primary, Shapiro, Jordan M., additional, Hollister, Emily B., additional, Badu, Shyam, additional, Wu, Qinglong, additional, Weidler, Erica M., additional, Abraham, Bincy P., additional, Devaraj, Sridevi, additional, Luna, Ruth Ann, additional, Versalovic, James, additional, Heitkemper, Margaret M., additional, Savidge, Tor C., additional, and Shulman, Robert J., additional

Published
2021
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18. A genomic catalog of Earth’s microbiomes

Author

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium

Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Published
2021

21. Promoting Cardiovascular Health in Early Childhood and Transitions in Childhood through Adolescence: A Workshop Report

Author

Daniels, Stephen R., Pratt, Charlotte A., Hollister, Emily B., Labarthe, Darwin, Cohen, Deborah A., Walker, Jenelle R., Beech, Bettina M., Balagopal, P. Babu, Beebe, Dean W., Gillman, Matthew W., Goodrich, Jaclyn M., Jaquish, Cashell, Kit, Brian, Miller, Alison L., Olds, David, Oken, Emily, Rajakumar, Kumaravel, Sherwood, Nancy E., Spruijt-Metz, Donna, Steinberger, Julia, Suglia, Shakira F., Teitelbaum, Susan L., Urbina, Elaine M., Van Horn, Linda, Ward, Dianne, and Young, Martin E.

Published
2019
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22. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method

Author

Santiago-Rodriguez, Tasha M., primary, Garoutte, Aaron, additional, Adams, Emmase, additional, Nasser, Waleed, additional, Ross, Matthew C., additional, La Reau, Alex, additional, Henseler, Zachariah, additional, Ward, Tonya, additional, Knights, Dan, additional, Petrosino, Joseph F., additional, and Hollister, Emily B., additional

Published
2020
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24. Can prescribed fires restore C4 grasslands invaded by a C3 woody species and a co‐dominant C3 grass species?

Author

Ansley, R. James, Boutton, Thomas W., and Hollister, Emily B.

Subjects
GRASSLANDS, PRESCRIBED burning, CHEATGRASS brome, GRASSLAND soils, PLANT invasions, WOODY plants, SPECIES
Abstract

Prescribed fire is used to reduce woody plant invasion and restore herbaceous production and diversity in grasslands and savannas worldwide. Here, we determined whether a concentrated series of repeated‐winter, repeated‐summer, or alternate‐season (winter and summer) fires in a short timeframe ("transition fires") could catalyze the restoration of C4 perennial grasses in Southern Great Plains, USA grasslands that had become dominated by a fire‐tolerant C3 woody N2‐fixer (honey mesquite, Prosopis glandulosa) and a C3 perennial bunchgrass (Texas wintergrass, Nassella leucotricha). We applied transition fires over a 5‐yr span and maintenance fires on a portion of each plot 7 or 8 yr later. We measured herbaceous standing biomass and cover and soil variables (soil organic C, N, δ13C, and δ15N) in unburned, transition‐burned, and maintenance‐burned treatments. Greater δ13C at 10–20 (−17‰) than 0–10 (−20‰) cm depth increment confirmed that vegetation was historically mostly C4 grassland that shifted toward C3 dominance. Transition treatments with summer fire were most effective at top‐killing mesquite, but no treatments root‐killed >3%. Regrowth of top‐killed mesquite was similar in all treatments and reached pre‐fire height by 9–10 yr post‐fire. Herbaceous production and cover responses showed that: (1) Alternate‐season transition fires increased C4 mid‐grass, but did not change Texas wintergrass; (2) repeated‐summer fires reduced Texas wintergrass, but did not change C4 mid‐grass; and (3) repeated‐winter fires did not change C4 mid‐grass or Texas wintergrass compared with the unburned control. All maintenance fires stimulated Texas wintergrass biomass and cover, thus eliminating the reduction of Texas wintergrass caused by repeated‐summer transition fires. There were no long‐term effects of transition fires on soil C, N, δ13C, or δ15N. Results advance our understanding of the expectations and limitations of prescribed fire in shifting a woodland alternate state toward what was historically a fire supported C4 grassland/savanna. [ABSTRACT FROM AUTHOR]

Published
2021
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25. Biochemical but not compositional recovery of skin mucosal microbiome communities after disruption

Author

Brumlow,Chelcy E., Luna,Ruth A., Hollister,Emily B., Gomez,Javier A., Burcham,Lindsey A., Cowdrey,Madison B., and Primm,Todd P.

Subjects
Infection and Drug Resistance
Abstract

Chelcy E Brumlow,1 Ruth A Luna,2,3 Emily B Hollister,2,3 Javier A Gomez,1 Lindsey A Burcham,1 Madison B Cowdrey,1 Todd P Primm1 1Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA; 2Department of Pathology, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX, USA; 3Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA Background: The microbiomes of animals are complex communities that strongly affect the health of the hosts. Microbiomes on mucosal surfaces have the highest densities and most extensive biochemical exchanges with the hosts. Although antibiotics are potent tools to manage infections, they can disrupt the normal microbiota, causing numerous side effects. Materials and methods: Taking a community ecology approach, mucosal microbiome community responses to five disruptive conditions (two broad-spectrum antibiotics, a biocide, elevated temperature, and rinsing) were analyzed. Skin of the fish Gambusia affinis was the mucosal model. Microbiome recovery was measured by culturable counts, community biochemical profiles, genetic fingerprinting, and community 16S gene sequencing (rinsing condition only). Results: Following all disruptions, the total counts rose and then returned to the pre-treatment (PT) level. This overgrowth was confirmed via direct staining and community metabolic activity measurements. After rinsing, diversity decreased and one taxon dominated (family Aeromonadaceae) temporarily, the findings similar to numerous other studies with antibiotics. While the community did not return to the PT taxonomic composition, the biochemical profile did. Conclusion: This suggests that the biochemical pathways in a community are important during recovery, and a return to the original composition is not required to restore original function. Keywords: Gambusia affinis, rifampicin, tetracycline, chlorhexidine

Published
2019

27. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome

Author

Hollister, Emily B., primary, Oezguen, Numan, additional, Chumpitazi, Bruno P., additional, Luna, Ruth Ann, additional, Weidler, Erica M., additional, Rubio-Gonzales, Michelle, additional, Dahdouli, Mahmoud, additional, Cope, Julia L., additional, Mistretta, Toni-Ann, additional, Raza, Sabeen, additional, Metcalf, Ginger A., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Petrosino, Joseph F., additional, Heitkemper, Margaret, additional, Savidge, Tor C., additional, Shulman, Robert J., additional, and Versalovic, James, additional

Published
2019
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30. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

Author

Pammi, Mohan, Cope, Julia, Tarr, Phillip I., Warner, Barbara B., Morrow, Ardythe L., Mai, Volker, Gregory, Katherine E., Kroll, J. Simon, McMurtry, Valerie, Ferris, Michael J, Engstrand, Lars, Lilja, Helene Engstrand, Hollister, Emily B., Versalovic, James, Neu, Josef, and Winnicott Foundation

Subjects
Firmicutes, Review, Infant, Premature, Diseases, Pediatrics, Microbiology in the medical area, Feces, Neonate, Preterm, Enterocolitis, Necrotizing, RNA, Ribosomal, 16S, Proteobacteria, Mikrobiologi inom det medicinska området, Bacteroides, Humans, Bacteria, NEC, Infant, Newborn, Pediatrik, digestive system diseases, 16S rRNA sequencing, Gastrointestinal Microbiome, Intestines, Intestinal, Dysbiosis, Microbiome, Infant, Premature
Abstract

Background Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results. Methods and results Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5). Conclusions Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC. Electronic supplementary material The online version of this article (doi:10.1186/s40168-017-0248-8) contains supplementary material, which is available to authorized users.

Published
2017

32. 80 - Microbial Multi-Omics Differentiates Children with Irritable Bowel Syndrome from Healthy Controls

Author

Hollister, Emily B., primary, Oezguen, Numan, additional, Chumpitazi, Bruno P., additional, Luna, Ruth Ann, additional, Weidler, Erica M., additional, Rubio-Gonzales, Michelle, additional, Dahdouli, Mahmoud, additional, Cope, Julia L., additional, Mistretta, Toni-Ann, additional, Raza, Sabeen, additional, Metcalf, Ginger A., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Petrosino, Joseph F., additional, Heitkemper, Margaret, additional, Savidge, Tor C., additional, Shulman, Robert J., additional, and Versalovic, James, additional

Published
2018
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34. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

Author

Schloss, Patrick D., Westcott, Sarah L., Ryabin, Thomas, Hall, Justine R., Hartmann, Martin, Hollister, Emily B., Lesniewski, Ryan A., Oakley, Brian B., Parks, Donovan H., Robinson, Courtney J., Sahl, Jason W., Stres, Blaz, Thallinger, Gerhard G., Van Horn, David J., and Weber, Carolyn F.

Subjects
Nucleotide sequence -- Analysis, Marine microbiology -- Research, Microbial genetics -- Research, Public software -- Usage, Ribosomal RNA -- Research, Open source software, Biological sciences
Abstract

A single software platform, mothur, is used to trim, screen, and align sequences, calculate distances, assign sequences to operational taxonomic units and also to describe the [alpha] and [beta] diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. The analysis of the huge sequence is completed in less than 2 hours with a laptop computer.

Published
2009

37. Reply

Author

Shulman, Robert J., primary, Hollister, Emily B., additional, Cain, Kevin, additional, and Heitkemper, Margaret, additional

Published
2016
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47. Structure and function of the healthy pre-adolescent pediatric gut microbiome

Author

Hollister, Emily B., primary, Riehle, Kevin, additional, Luna, Ruth Ann, additional, Weidler, Erica M., additional, Rubio-Gonzales, Michelle, additional, Mistretta, Toni-Ann, additional, Raza, Sabeen, additional, Doddapaneni, Harsha V., additional, Metcalf, Ginger A., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Petrosino, Joseph F., additional, Shulman, Robert J., additional, and Versalovic, James, additional

Published
2015
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