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Fernandez Trigo N, Kalbermatter C, Yilmaz B, Ganal-Vonarburg SC. The protective effect of the intestinal microbiota in type-1 diabetes in NOD mice is limited to a time window in early life. Front Endocrinol (Lausanne) 2024; 15:1425235. [PMID: 39391872 PMCID: PMC11464356 DOI: 10.3389/fendo.2024.1425235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024] Open
Abstract
Introduction The incidence of type-1 diabetes is on the rise, particularly in developed nations, and predominantly affects the youth. While genetic predisposition plays a substantial role, environmental factors, including alterations in the gut microbiota, are increasingly recognized as significant contributors to the disease. Methods In this study, we utilized germ-free non-obese diabetic mice to explore the effects of microbiota colonization during early life on type-1 diabetes susceptibility. Results Our findings reveal that microbiota introduction at birth, rather than at weaning, significantly reduces the risk of type-1 diabetes, indicating a crucial window for microbiota-mediated modulation of immune responses. This protective effect was independent of alterations in intestinal barrier function but correlated with testosterone levels in male mice. Additionally, early life colonization modulated T cell subset frequencies, particularly T helper cells and regulatory T cells, in the intestine, potentially shaping type-1 diabetes predisposition. Discussion Our findings underscore the pivotal role of early-life microbial interactions in immune regulation and the development of autoimmune diseases.
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Affiliation(s)
- Nerea Fernandez Trigo
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Cristina Kalbermatter
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Stephanie C. Ganal-Vonarburg
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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2
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Johansson Å, Subramani MV, Yilmaz B, Nyström E, Layunta E, Arike L, Sommer F, Rosenstiel P, Vereecke L, Holm LM, Wullaert A, Pelaseyed T, Johansson MEV, Birchenough GMH. Neonatal microbiota colonization drives maturation of primary and secondary goblet cell mediated protection in the pre-weaning colon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601781. [PMID: 39005291 PMCID: PMC11245021 DOI: 10.1101/2024.07.03.601781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In the distal colon, mucus secreting goblet cells primarily confer protection from luminal microorganisms via generation of a sterile inner mucus layer barrier structure. Bacteria-sensing sentinel goblet cells provide a secondary defensive mechanism that orchestrates mucus secretion in response to microbes that breach the mucus barrier. Previous reports have identified mucus barrier deficiencies in adult germ-free mice, thus implicating a fundamental role for the microbiota in programming mucus barrier generation. In this study, we have investigated the natural neonatal development of the mucus barrier and sentinel goblet cell-dependent secretory responses upon postnatal colonization. Combined in vivo and ex vivo analyses of pre- and post-weaning colonic mucus barrier and sentinel goblet cell maturation demonstrated a sequential microbiota-dependent development of these primary and secondary goblet cell-intrinsic protective functions, with dynamic changes in mucus processing dependent on innate immune signalling via MyD88, and development of functional sentinel goblet cells dependent on the NADPH/Dual oxidase family member Duox2. Our findings therefore identify new mechanisms of microbiota-goblet cell regulatory interaction and highlight the critical importance of the pre-weaning period for the normal development of colonic barrier function.
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3
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Kim TS, Ikeuchi T, Theofilou VI, Williams DW, Greenwell-Wild T, June A, Adade EE, Li L, Abusleme L, Dutzan N, Yuan Y, Brenchley L, Bouladoux N, Sakamachi Y, Palmer RJ, Iglesias-Bartolome R, Trinchieri G, Garantziotis S, Belkaid Y, Valm AM, Diaz PI, Holland SM, Moutsopoulos NM. Epithelial-derived interleukin-23 promotes oral mucosal immunopathology. Immunity 2024; 57:859-875.e11. [PMID: 38513665 PMCID: PMC11058479 DOI: 10.1016/j.immuni.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/05/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
At mucosal surfaces, epithelial cells provide a structural barrier and an immune defense system. However, dysregulated epithelial responses can contribute to disease states. Here, we demonstrated that epithelial cell-intrinsic production of interleukin-23 (IL-23) triggers an inflammatory loop in the prevalent oral disease periodontitis. Epithelial IL-23 expression localized to areas proximal to the disease-associated microbiome and was evident in experimental models and patients with common and genetic forms of disease. Mechanistically, flagellated microbial species of the periodontitis microbiome triggered epithelial IL-23 induction in a TLR5 receptor-dependent manner. Therefore, unlike other Th17-driven diseases, non-hematopoietic-cell-derived IL-23 served as an initiator of pathogenic inflammation in periodontitis. Beyond periodontitis, analysis of publicly available datasets revealed the expression of epithelial IL-23 in settings of infection, malignancy, and autoimmunity, suggesting a broader role for epithelial-intrinsic IL-23 in human disease. Collectively, this work highlights an important role for the barrier epithelium in the induction of IL-23-mediated inflammation.
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Affiliation(s)
- Tae Sung Kim
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tomoko Ikeuchi
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vasileios Ionas Theofilou
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA; Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
| | - Drake Winslow Williams
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Teresa Greenwell-Wild
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Armond June
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, University at Buffalo, Buffalo, NY 14214, USA
| | - Emmanuel E Adade
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12210, USA
| | - Lu Li
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, University at Buffalo, Buffalo, NY 14214, USA
| | - Loreto Abusleme
- Department of Pathology and Oral Medicine, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Nicolas Dutzan
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Yao Yuan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurie Brenchley
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yosuke Sakamachi
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert J Palmer
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramiro Iglesias-Bartolome
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stavros Garantziotis
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alex M Valm
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12210, USA
| | - Patricia I Diaz
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, University at Buffalo, Buffalo, NY 14214, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Niki M Moutsopoulos
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
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5
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Kortman GAM, Timmerman HM, Schaafsma A, Stoutjesdijk E, Muskiet FAJ, Nhien NV, van Hoffen E, Boekhorst J, Nauta A. Mothers' Breast Milk Composition and Their Respective Infant's Gut Microbiota Differ between Five Distinct Rural and Urban Regions in Vietnam. Nutrients 2023; 15:4802. [PMID: 38004196 PMCID: PMC10675055 DOI: 10.3390/nu15224802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Microbiota colonization and development in early life is impacted by various host intrinsic (genetic) factors, but also diet, lifestyle, as well as environmental and residential factors upon and after birth. To characterize the impact of maternal nutrition and environmental factors on vaginally born infant gut microbiota composition, we performed an observational study in five distinct geographical areas in Vietnam. Fecal samples of infants (around 39 days old) and fecal and breast milk samples of their mothers (around 28 years) were collected. The microbiota composition of all samples was analyzed by 16S rRNA gene Illumina sequencing and a bioinformatics workflow based on QIIME. In addition, various breast milk components were determined. Strong associations between the geographically determined maternal diet and breast milk composition as well as infant fecal microbiota were revealed. Most notable was the association of urban Ha Noi with relatively high abundances of taxa considered pathobionts, such as Klebsiella and Citrobacter, at the expense of Bifidobacterium. Breast milk composition was most distinct in rural Ha Long Bay, characterized by higher concentrations of, e.g., docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), selenium, and vitamin B12, while it was characterized by, e.g., iron, zinc, and α-linolenic acid (ALA) in Ha Noi. Breast milk iron levels were positively associated with infant fecal Klebsiella and negatively with Bifidobacterium, while the EPA and DHA levels were positively associated with Bifidobacterium. In conclusion, differences between five regions in Vietnam with respect to both maternal breast milk and infant gut microbiota composition were revealed, most likely in part due to maternal nutrition. Thus, there could be opportunities to beneficially steer infant microbiota development in a more desired (rural instead of urban) direction through the mother's diet.
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Affiliation(s)
| | | | - Anne Schaafsma
- Friesland Campina, Stationsplein 4, 3818 LE Amersfoort, The Netherlands
| | - Eline Stoutjesdijk
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Frits A. J. Muskiet
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Nguyen V. Nhien
- National Institute of Food Control, No. 65 Pham Than Duat Str., Mai Dich Ward., Cau Giay Dist., Ha Noi 100000, Vietnam
| | | | - Jos Boekhorst
- NIZO Food Research B.V., 6718 ZB Ede, The Netherlands
| | - Arjen Nauta
- Friesland Campina, Stationsplein 4, 3818 LE Amersfoort, The Netherlands
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6
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Campisciano G, Zanotta N, Quadrifoglio M, Careri A, Torresani A, Cason C, De Seta F, Ricci G, Comar M, Stampalija T. The Bacterial DNA Profiling of Chorionic Villi and Amniotic Fluids Reveals Overlaps with Maternal Oral, Vaginal, and Gut Microbiomes. Int J Mol Sci 2023; 24:ijms24032873. [PMID: 36769194 PMCID: PMC9917689 DOI: 10.3390/ijms24032873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The in utero microbiome hypothesis has been long debated. This hypothesis will change our comprehension of the pioneer human microbiome if proved correct. In 60 uncomplicated pregnancies, we profiled the microbiome of chorionic villi (CV) and amniotic fluids (AF) in relation to maternal saliva, rectum, and vagina and the soluble cytokines cascade in the vagina, CV and AF. In our series, 12/37 (32%) AF and 10/23 (44%) CV tested positive for bacterial DNA. CV and AF harbored bacterial DNA of Streptococcus and Lactobacillus, overlapping that of the matched oral and vaginal niches, which showed a dysbiotic microbiome. In these pregnant women, the immune profiling revealed an immune hyporesponsiveness in the vagina and a high intraamniotic concentration of inflammatory cytokines. To understand the eventual role of bacterial colonization of the CV and AF and the associated immune response in the pregnancy outcome, further appropriate studies are needed. In this context, further studies should highlight if the hematogenous route could justify the spread of bacterial DNA from the oral microbiome to the placenta and if vaginal dysbiosis could favor the likelihood of identifying CV and AF positive for bacterial DNA.
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Affiliation(s)
- Giuseppina Campisciano
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
- Correspondence:
| | - Nunzia Zanotta
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
| | - Mariachiara Quadrifoglio
- Unit of Fetal Medicine and Prenatal Diagnosis, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
| | - Annalisa Careri
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Alessandra Torresani
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Carolina Cason
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
| | - Francesco De Seta
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
- Department of Obstetrics and Gynecology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
| | - Giuseppe Ricci
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
- Department of Obstetrics and Gynecology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
| | - Manola Comar
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Tamara Stampalija
- Unit of Fetal Medicine and Prenatal Diagnosis, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Via dell’Istria, 65, 34137 Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
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7
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Yilmaz B, Fuhrer T, Morgenthaler D, Krupka N, Wang D, Spari D, Candinas D, Misselwitz B, Beldi G, Sauer U, Macpherson AJ. Plasticity of the adult human small intestinal stoma microbiota. Cell Host Microbe 2022; 30:1773-1787.e6. [PMID: 36318918 DOI: 10.1016/j.chom.2022.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Abstract
The human distal small intestine (ileum) has a distinct microbiota, but human studies investigating its composition and function have been limited by the inaccessibility of the ileum without purging and/or deep intubation. We investigated inherent instability, temporal dynamics, and the contribution of fed and fasted states using stoma samples from cured colorectal cancer patients as a non-invasive access route to the otherwise inaccessible small and large intestines. Sequential sampling of the ileum before and after stoma formation indicated that ileostoma microbiotas represented that of the intact small intestine. Ileal and colonic stoma microbiotas were confirmed as distinct, and two types of instability in ileal host-microbial relationships were observed: inter-digestive purging followed by the rapid postprandial blooming of bacterial biomass and sub-strain appearance and disappearance within individual taxa after feeding. In contrast to the relative stability of colonic microbiota, the human small intestinal microbiota biomass and its sub-strain composition can be highly dynamic.
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Affiliation(s)
- Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3008 Bern, Switzerland.
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Deborah Morgenthaler
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Niklas Krupka
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Daniel Spari
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Daniel Candinas
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Benjamin Misselwitz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Guido Beldi
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Andrew J Macpherson
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3008 Bern, Switzerland.
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8
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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9
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Schneider R, Kraljević M, Peterli R, Rohm TV, Bosch AJ, Low AJ, Keller L, AlAsfoor S, Häfliger S, Yilmaz B, Peterson CJ, Lazaridis II, Vonaesch P, Delko T, Cavelti-Weder C. Roux-en-Y gastric bypass with a long compared to a short biliopancreatic limb improves weight loss and glycemic control in obese mice. Surg Obes Relat Dis 2022; 18:1286-1297. [DOI: 10.1016/j.soard.2022.06.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022]
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10
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Multi-Agent Simulation of Product Diffusion in Online Social Networks from the Perspective of Overconfidence and Network Effects. SUSTAINABILITY 2022. [DOI: 10.3390/su14116589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Online social networks (OSNs) have steadily become the primary mechanism of product promotion. However, previous studies have paid little concern to the irrational consumer behavior (e.g., overconfidence) and network effects that influence product diffusion in OSNs. We use overconfidence theory, network effects theory, and evolutionary game theory to build a multi-agent simulation model that captures the nonlinear relationship between individual actions to examine the effects of overconfidence and network effects on product diffusion in OSNs. We found that (1) overestimation is profitable for improving the diffusion level of product diffusion in OSNs and maintaining market stability; however, the closer the degree of overprecision is to 1 (i.e., individuals are more rational), the more stable the market will be. We also found that (2) moderate network effect intensity can better promote product diffusion on the social network. When the network effect intensity is small, the non-overconfident scenario has the highest percentage of adoption. The overprecision scenario has the highest percentage of adoption where the network effect intensity is high. Additionally, we found that (3) the scale-free network is more conducive to the diffusion of products in OSNs, while the small-world network is more susceptible to overconfidence and network effect. This research laid the groundwork for investigating dynamic consumer behavior utilizing a multi-agent method, network effects theory, and a psychological theory.
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11
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Rohm TV, Keller L, Bosch AJT, AlAsfoor S, Baumann Z, Thomas A, Wiedemann SJ, Steiger L, Dalmas E, Wehner J, Rachid L, Mooser C, Yilmaz B, Fernandez Trigo N, Jauch AJ, Wueest S, Konrad D, Henri S, Niess JH, Hruz P, Ganal-Vonarburg SC, Roux J, Meier DT, Cavelti-Weder C. Targeting colonic macrophages improves glycemic control in high-fat diet-induced obesity. Commun Biol 2022; 5:370. [PMID: 35440795 PMCID: PMC9018739 DOI: 10.1038/s42003-022-03305-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
The obesity epidemic continues to worsen worldwide. However, the mechanisms initiating glucose dysregulation in obesity remain poorly understood. We assessed the role that colonic macrophage subpopulations play in glucose homeostasis in mice fed a high-fat diet (HFD). Concurrent with glucose intolerance, pro-inflammatory/monocyte-derived colonic macrophages increased in mice fed a HFD. A link between macrophage numbers and glycemia was established by pharmacological dose-dependent ablation of macrophages. In particular, colon-specific macrophage depletion by intrarectal clodronate liposomes improved glucose tolerance, insulin sensitivity, and insulin secretion capacity. Colonic macrophage activation upon HFD was characterized by an interferon response and a change in mitochondrial metabolism, which converged in mTOR as a common regulator. Colon-specific mTOR inhibition reduced pro-inflammatory macrophages and ameliorated insulin secretion capacity, similar to colon-specific macrophage depletion, but did not affect insulin sensitivity. Thus, pharmacological targeting of colonic macrophages could become a potential therapy in obesity to improve glycemic control. Expansion of pro-inflammatory macrophages in the colon occurs early after high-fat diet initiation, prior to macrophage accumulation in the adipose tissue, in a microbiome-dependent fashion. Macrophage depletion systemically and/or exclusively in the colon improves glucose metabolism.
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Affiliation(s)
- Theresa V Rohm
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Lena Keller
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Angela J T Bosch
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Shefaa AlAsfoor
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Zora Baumann
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | | | - Sophia J Wiedemann
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Laura Steiger
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Elise Dalmas
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Josua Wehner
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Leila Rachid
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Catherine Mooser
- Department of Visceral Surgery und Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Bahtiyar Yilmaz
- Department of Visceral Surgery und Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Nerea Fernandez Trigo
- Department of Visceral Surgery und Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Annaise J Jauch
- Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Stephan Wueest
- Division of Pediatric Endocrinology and Diabetology, and Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Daniel Konrad
- Division of Pediatric Endocrinology and Diabetology, and Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Jan H Niess
- Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Center for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Petr Hruz
- Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Center for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Department of Visceral Surgery und Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Julien Roux
- Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Daniel T Meier
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Claudia Cavelti-Weder
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Basel, Switzerland. .,Department of Biomedicine (DBM), University of Basel, University Hospital Basel, Basel, Switzerland. .,Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland.
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12
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Choudhury N, Siddiqua TJ, Ahmed SMT, Haque MA, Ali M, Dil Farzana F, Naz F, Rahman SS, Faruque ASG, Rahman S, Ahmed T. Iron content of drinking water is associated with anaemia status among children in high groundwater iron areas in Bangladesh. Trop Med Int Health 2021; 27:149-157. [PMID: 34905267 DOI: 10.1111/tmi.13710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Iron in groundwater provides a good source of absorbable iron for humans and can contribute to optimal iron and haemoglobin (Hb) status among populations. We aimed to examine the relationship between the iron content of groundwater and anaemia status among 12- to 23-month-old children in a rural area of Bangladesh. METHOD A cross-sectional study was conducted in 80 randomly selected unions (the lowest administrative unit) in Sylhet and Moulvibazar districts of Bangladesh. A total of 800 children aged 12-23 months were selected via a systematic random sampling method. The child's age, sex, stunting status, consumption of iron-rich or iron-fortified food, maternal age and maternal body mass index (BMI) and the type of terrain were subjected to multiple logistic regression analysis to observe the independent relationships between groundwater iron content and anaemia in children. RESULTS In total, 50.4% of children were anaemic. The odds of children being anaemic were 1.51-fold higher [OR: 1.51 (95% CI: 1.09, 2.09)] among households consuming water with an iron content <2 mg/L than in households consuming water with an iron content ≥2 mg/L. Childhood stunting, child's sex, child's age and the type of terrain were also significantly associated with anaemia among children. CONCLUSION Groundwater with a high iron concentration was significantly associated with a decreased risk of childhood anaemia. This study provides evidence of the importance of groundwater iron to protect impoverished young children from anaemia.
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Affiliation(s)
- Nuzhat Choudhury
- Nutrition and Clinical Services Division, ICDDR,B, Dhaka, Bangladesh
| | | | | | - Md Ahshanul Haque
- Nutrition and Clinical Services Division, ICDDR,B, Dhaka, Bangladesh
| | - Mohammad Ali
- Nutrition and Clinical Services Division, ICDDR,B, Dhaka, Bangladesh
| | | | - Farina Naz
- Nutrition and Clinical Services Division, ICDDR,B, Dhaka, Bangladesh
| | | | - A S G Faruque
- Nutrition and Clinical Services Division, ICDDR,B, Dhaka, Bangladesh
| | | | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, ICDDR,B, Dhaka, Bangladesh
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13
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Lopez-Pier MA, Koppinger MP, Harris PR, Cannon DK, Skaria RS, Hurwitz BL, Watts G, Aras S, Slepian MJ, Konhilas JP. An adaptable and non-invasive method for tracking Bifidobacterium animalis subspecies lactis 420 in the mouse gut. J Microbiol Methods 2021; 189:106302. [PMID: 34391819 PMCID: PMC8473990 DOI: 10.1016/j.mimet.2021.106302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 11/26/2022]
Abstract
Probiotic strains from the Bifidobacterium or Lactobacillus genera improve health outcomes in models of metabolic and cardiovascular disease. Yet, underlying mechanisms governing these improved health outcomes are rooted in the interaction of gut microbiota, intestinal interface, and probiotic strain. Central to defining the underlying mechanisms governing these improved health outcomes is the development of adaptable and non-invasive tools to study probiotic localization and colonization within the host gut microbiome. The objective of this study was to test labeling and tracking efficacy of Bifidobacterium animalis subspecies lactis 420 (B420) using a common clinical imaging agent, indocyanine green (ICG). ICG was an effective in situ labeling agent visualized in either intact mouse or excised gastrointestinal (GI) tract at different time intervals. Quantitative PCR was used to validate ICG visualization of B420, which also demonstrated that B420 transit time matched normal murine GI motility (~8 hours). Contrary to previous thoughts, B420 did not colonize any region of the GI tract whether following a single bolus or daily administration for up to 10 days. We conclude that ICG may provide a useful tool to visualize and track probiotic species such as B420 without implementing complex molecular and genetic tools. Proof-of-concept studies indicate that B420 did not colonize and establish residency align the murine GI tract.
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Affiliation(s)
- Marissa A Lopez-Pier
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA
| | - Matthew P Koppinger
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Nutritional Sciences, University of Arizona, Tucson, AZ, USA
| | - Preston R Harris
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Nutritional Sciences, University of Arizona, Tucson, AZ, USA
| | - Danielle K Cannon
- Department of Physiology, University of Arizona, Tucson, AZ, USA; Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA
| | - Rinku S Skaria
- Department of Physiology, University of Arizona, Tucson, AZ, USA; Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA
| | | | - George Watts
- Bio5 Institute, University of Arizona, Tucson, AZ, USA
| | | | - Marvin J Slepian
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA; Bio5 Institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - John P Konhilas
- Department of Physiology, University of Arizona, Tucson, AZ, USA; Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA; Department of Nutritional Sciences, University of Arizona, Tucson, AZ, USA.
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14
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Abou Chacra L, Fenollar F. Exploring the global vaginal microbiome and its impact on human health. Microb Pathog 2021; 160:105172. [PMID: 34500016 DOI: 10.1016/j.micpath.2021.105172] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/19/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023]
Abstract
Around the world, more than 175,000,000 women are diagnosed every year with gynaecological disease, in many cases contributing to high morbidity and mortality. For this reason, knowledge of the composition of the vaginal microbiome and its variations represents a real health challenge, as this is key to improving therapeutic management. This review traces the history of the poorly known vaginal microbiome and focuses on the latest findings concerning this ecosystem. Studies in the past decade have targeted complex bacterial communities within the vagina. However, due to the development of technology and the emergence of next generation sequencing (NGS), the exact definition of the vaginal microbiome has changed and can no longer be linked solely to the presence of bacteria. In order to reach a global view of the vaginal microbiome, it is essential to take into account all microorganisms that the vagina harbours, including fungi, viruses, archaea, and candidate phyla radiation. Although these communities represent only a minimal percentage of the vaginal microbiome, they may act as modifiers of its basic physiology and may play a key role in the maintenance of microbial communities, as well as metabolic and immune functions. Studies of the complex interactions between these different microorganisms have recently begun and are not yet fully understood. Results to date indicate that these microbial communities together constitute the first line of defence against infections. On the other hand, the slightest disturbance in this microbiome may lead to disease. For this reason, enhanced knowledge of these associations is critical to better identify predispositions to certain illnesses, which may open new therapeutic avenues. Currently however, only the tip of the iceberg is understood and current research on this ecosystem is revolutionising our knowledge and understanding of human health and disease.
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Affiliation(s)
- Linda Abou Chacra
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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15
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Modulation of the Mucosa-Associated Microbiome Linked to the PTPN2 Risk Gene in Patients with Primary Sclerosing Cholangitis and Ulcerative Colitis. Microorganisms 2021; 9:microorganisms9081752. [PMID: 34442830 PMCID: PMC8399714 DOI: 10.3390/microorganisms9081752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/31/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022] Open
Abstract
Gut microbiota appears to be involved in the pathogenesis of primary sclerosing cholangitis (PSC). The protein tyrosine phosphatase nonreceptor 2 (PTPN2) gene risk variant rs1893217 is associated with gut dysbiosis in inflammatory bowel disease (IBD), and PTPN2 was mentioned as a possible risk gene for PSC. This study assessed the microbial profile of ulcerative colitis (UC) patients with PSC and without PSC (non-PSC). Additionally, effects of the PTPN2 risk variant were assessed. In total, 216 mucosal samples from ileum, colon, and rectum were collected from 7 PSC and 42 non-PSC patients, as well as 28 control subjects (non-IBD). The microbial composition was derived from 16S rRNA sequencing data. Overall, bacterial richness was highest in PSC patients, who also had a higher relative abundance of the genus Roseburia compared to non-PSC, as well as Haemophilus, Fusobacterium, Bifidobacterium, and Actinobacillus compared to non-IBD, as well as a lower relative abundance of Bacteroides compared to non-PSC and non-IBD, respectively. After exclusion of patients with the PTPN2 risk variant, Brachyspira was higher in PSC compared to non-PSC, while, solely in colon samples, Eubacterium and Tepidimonas were higher in PSC vs. non-IBD. In conclusion, this study underlines the presence of gut mucosa-associated microbiome changes in PSC patients and rather weakens the role of PTPN2 as a PSC risk gene.
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16
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Microbial Contamination in Hospital Environment Has the Potential to Colonize Preterm Newborns' Nasal Cavities. Pathogens 2021; 10:pathogens10050615. [PMID: 34067889 PMCID: PMC8156200 DOI: 10.3390/pathogens10050615] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/29/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
Infants born before 28 weeks are at risk of contracting healthcare-associated infections (HAIs), which could be caused by pathogens residing on contaminated hospital surfaces. In this longitudinal study, we characterized by NGS the bacterial composition of nasal swabs of preterm newborns, at the time of birth and after admission to the Neonatal Intensive Care Unit (NICU), comparing it with that of the environmental wards at the time of delivery and during the hospitalization. We characterized the resistome on the samples too. The results showed that environmental microorganisms responsible for HAIs, in particular Staphylococcus spp., Streptococcus spp., Escherichia-Shigella spp., and K. pneumoniae, were detected in higher percentages in the noses of the babies after 13 days of hospitalization, in terms of the number of colonized patients, microorganism amount, and relative abundance. The analysis of nasal bacteria resistome evidenced the absence of resistance genes at the time of birth, some of which appeared and increased after the admission in the NICU. These data suggest that hospital surface microbiota might be transported to respiratory mucosae or other profound tissues. Our study highlights the importance of a screening that allows characterizing the microbial profile of the environment to assess the risk of colonization of the newborn.
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17
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Rahman S, Kortman GAM, Boekhorst J, Lee P, Khan MR, Ahmed F. Effect of low-iron micronutrient powder (MNP) on the composition of gut microbiota of Bangladeshi children in a high-iron groundwater setting: a randomized controlled trial. Eur J Nutr 2021; 60:3423-3436. [PMID: 33634319 PMCID: PMC8354964 DOI: 10.1007/s00394-021-02523-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/16/2021] [Indexed: 12/25/2022]
Abstract
Purpose Adverse effects of iron fortification/supplements such as Micronutrient Powder (MNP) on gut microbiota have previously been found in infection-prone African settings. This study examined the adversaries of a low-iron MNP compared with the standard MNP on the composition of gut microbiota in Bangladeshi children exposed to a high concentration of iron from potable groundwater. Methods A randomized controlled trial was conducted in 2- to 5-year-old children, drinking groundwater with a high concentration of iron (≥ 2 mg/L). Children were randomized to receive one sachet per day of either standard MNP (12.5 mg iron) or low-iron MNP (5 mg iron), for 2 months. A sub-sample of 53 children was considered for paired assessment of the gut microbiome by 16S rRNA amplicon sequencing. Results At baseline, the gut microbiota consisted of Bifidobacteriaceae (15.6%), Prevotellaceae (12.2%), Lactobacillaceae (3.6%), Clostridiaceae (4.1%) and Enterobacteriaceae (2.8%). Overall, there was no significant treatment effect of the low-iron MNP compared to the standard MNP. However, an apparent treatment effect was observed in children with a relative adult-like microbiota, with a higher relative abundance of potentially pathogenic Enterobacteriaceae after receiving the standard MNP compared to the low-iron MNP. This effect, however, was statistically non-significant (p = 0.07). Conclusion In Bangladeshi children drinking iron-rich groundwater, a low-iron MNP supplementation did not have a significant impact on their gut microbiota profile/composition compared to the standard MNP. The trial registration number is ISRCTN60058115; Date of registration 03/07/2019; retrospectively registered. Supplementary Information The online version of this article (10.1007/s00394-021-02523-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabuktagin Rahman
- Public Health, School of Medicine, Griffith University, Gold Coast Campus, Parklands Dr., Gold Coast, QLD, 4222, Australia
| | | | - Jos Boekhorst
- NIZO Food Research B.V., Ede, The Netherlands
- Host-Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Patricia Lee
- Public Health, School of Medicine, Griffith University, Gold Coast Campus, Parklands Dr., Gold Coast, QLD, 4222, Australia
| | - Moududur R Khan
- Institute of Nutrition and Food Science, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Faruk Ahmed
- Public Health, School of Medicine, Griffith University, Gold Coast Campus, Parklands Dr., Gold Coast, QLD, 4222, Australia.
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18
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de Melo Pereira GV, de Carvalho Neto DP, Maske BL, De Dea Lindner J, Vale AS, Favero GR, Viesser J, de Carvalho JC, Góes-Neto A, Soccol CR. An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far? Crit Rev Food Sci Nutr 2020; 62:1870-1889. [PMID: 33207956 DOI: 10.1080/10408398.2020.1848787] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.
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Affiliation(s)
- Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Dão Pedro de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Bruna L Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Alexander S Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Gabriel R Favero
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Jéssica Viesser
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Júlio C de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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19
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Hamilton AL, Kamm MA, De Cruz P, Wright EK, Feng H, Wagner J, Sung JJY, Kirkwood CD, Inouye M, Teo SM. Luminal microbiota related to Crohn's disease recurrence after surgery. Gut Microbes 2020; 11:1713-1728. [PMID: 32564657 PMCID: PMC7524166 DOI: 10.1080/19490976.2020.1778262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Microbial factors are likely to be involved in the recurrence of Crohn's disease (CD) after bowel resection. We investigated the luminal microbiota before and longitudinally after surgery, in relation to disease recurrence, using 16S metagenomic techniques. METHODS In the prospective Post-Operative Crohn's Endoscopic Recurrence (POCER) study, fecal samples were obtained before surgery and 6, 12, and 18 months after surgery from 130 CD patients. Endoscopy was undertaken to detect disease recurrence, defined as Rutgeerts score ≥i2, at 6 months in two-thirds of patients and all patients at 18 months after surgery. The V2 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Cluster analysis was performed at family level, assessing microbiome community differences between patients with and without recurrence. RESULTS Six microbial cluster groups were identified. The cluster associated with maintenance of remission was enriched for the Lachnospiraceae family [adjusted OR 0.47 (0.27-0.82), P = .007]. The OTU diversity of Lachnospiraceae within this cluster was significantly greater than in all other clusters. The cluster enriched for Enterobacteriaceae was associated with an increased risk of disease recurrence [adjusted OR 6.35 (1.24-32.44), P = .026]. OTU diversity of Enterobacteriaceae within this cluster was significantly greater than in other clusters. CONCLUSIONS Luminal bacterial communities are associated with protection from, and the occurrence of, Crohn's disease recurrence after surgery. Recurrence may relate to a higher abundance of facultatively anaerobic pathobionts from the Enterobacteriaceae family. The ecologic change of depleted Lachnospiraceae, a genus of butyrate-producing bacteria, may permit expansion of Enterobacteriaceae through luminal environmental perturbation.
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Affiliation(s)
- Amy L. Hamilton
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Michael A. Kamm
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia,CONTACT Michael A. Kamm St Vincent’s Hospital, Melbourne, Australia
| | - Peter De Cruz
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia,Department of Gastroenterology, Austin Health, Melbourne, Australia
| | - Emily K. Wright
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Hai Feng
- The Chinese University of Hong Kong, Hong Kong, China,Enteric Virus Group, Murdoch Children’s Research Institute, Melbourne, Australia,School of Pharmacy, Harbin Medical University, Harbin, China
| | - Josef Wagner
- Enteric Virus Group, Murdoch Children’s Research Institute, Melbourne, Australia,Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, Melbourne, Australia
| | | | - Carl D. Kirkwood
- Enteric Virus Group, Murdoch Children’s Research Institute, Melbourne, Australia,Enteric and Diarrheal Diseases Global Health, Bill and Melinda Gates Foundation, SeattleUSA, WA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia and Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Shu-Mei Teo
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia and Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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20
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Zanotta N, Ottaviani G, Campisciano G, Poropat A, Bovenzi M, Rupel K, Gobbo M, Comar M, Di Lenarda R, Biasotto M, Zacchigna S. Photobiomodulation modulates inflammation and oral microbiome: a pilot study. Biomarkers 2020; 25:677-684. [PMID: 32960109 DOI: 10.1080/1354750x.2020.1825812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Oral mucositis (OM) is a severe side effect in patients undergoing anticancer therapies, which negatively impacts on their quality of life often leading to either the interruption of the therapy. Photobiomodulation (PBM) is emerging as an effective strategy allowing a faster wound healing. OBJECTIVES This pilot study aims at verifying whether PBM modulates the inflammatory response in patients and its effect on the oral microbiome composition. MATERIALS AND METHODS Buccal swabs were collected from four patients affected by OM, both on ulcerated and clinically healthy areas, before and on the last day of PBM therapy, as well as on the first day after treatment discontinuation. The concentration of 38 cytokines and the composition of oral microbiome were measured. RESULTS Most of the pro-inflammatory cytokines were reduced, whereas anti-inflammatory cytokines resulted up-regulated by PBM. In addition, PBM influenced the composition of oral microbiome, by decreasing the amount of pathogenic species and promoting the growth of commensal bacteria. These changes were even more evident when separately analysing patients who clinically responded to PBM and the only patient who did not respond. CONCLUSIONS PBM reduces inflammatory burden in patients affected by OM and positively influences the composition of the oral microbiome.
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Affiliation(s)
- Nunzia Zanotta
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Giulia Ottaviani
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | | | - Augusto Poropat
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Massimo Bovenzi
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Katia Rupel
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Margherita Gobbo
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Manola Comar
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Roberto Di Lenarda
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Matteo Biasotto
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Serena Zacchigna
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,International Centre for Genetic Engineering and Biotechnology (ICGEB), Cardiovascular Biology Laboratory, Trieste, Italy
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21
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Wasimuddin, Schlaeppi K, Ronchi F, Leib SL, Erb M, Ramette A. Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework. Mol Ecol Resour 2020; 20:1558-1571. [PMID: 32599660 PMCID: PMC7693082 DOI: 10.1111/1755-0998.13215] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022]
Abstract
The 'One Health' framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extraction kits and commonly recommended primer pairs targeting different hypervariable regions (V3-V4, V4, V5-V6, V5-V6-V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F-806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F-806R revealed that soil and root samples have the highest estimates of species richness, while lowest richness was observed in human faeces. Primer pair choice directly influenced the estimation of community changes within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.
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Affiliation(s)
- Wasimuddin
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Francesca Ronchi
- Department for Biomedical Research, University of Bern, Inselspital, Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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22
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Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during In Vitro Fertilization Surgery. mSystems 2020; 5:5/4/e00450-20. [PMID: 32665329 PMCID: PMC7363005 DOI: 10.1128/msystems.00450-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The microbiome had been hypothesized to be involved in the physiology and pathophysiology of assisted reproduction before the first success in IVF, while the data supporting or refuting this hypothesis were less than conclusive. Thanks to sequencing data from the 16S rRNA subunit, we characterized the microbiome in the reproductive tract of infertile women, and we found that changes in the vaginal microbiome are related to female infertility. We also found that the characteristic microbiome bacteria are mainly members of several genera and that the vaginal microbiome of infertile women is not sensitive to hormonal changes during IVF. In conclusion, our report provides data that can be used for discovering the role of the vaginal microbiome in patients suffering from secondary infertility. Perturbation of vaginal microbiome of reproductive-age women influences all the phases of a woman's reproductive life. Although studies have shown that dynamic changes in vaginal microbiome can affect pregnancy, its role in secondary infertility (i.e., inability to become pregnant or to carry a pregnancy successfully after previous success in delivering a child) and in vitrofertilization (IVF) remains to be unraveled. To determine the vaginal microbiome in women undergoing in vitrofertilization and embryo transfer (IVF-ET) and investigate its potential correlations with hormone stimulation, we recruited 30 patients with secondary infertility and receiving IVF and 92 matched healthy women and analyzed their vaginal microbiome composition using 16S rRNA gene sequencing. Our results show that women suffering from infertility (infertile women) exhibit a significant decrease in microbiome diversity and richness compared with healthy women during the nonovulation period (follicular phase) (P < 0.01), whereas vaginal microbiome of healthy women reveals dramatic fluctuations during ovulation (P < 0.05). Interestingly, infertility patients show no change of the vaginal microbiome under conditions of gonadotropin-releasing hormone (GnRH) agonist and recombinant human chorionic gonadotropin (r-hCG) induction (P > 0.05). Moreover, our results indicate that infertile women show characteristic variations in vaginal microbiome, such as increased abundance of Atopobium, Aerococcus, and Bifidobacterium and decreased abundance of Lactobacillus and Leuconostoc. IMPORTANCE The microbiome had been hypothesized to be involved in the physiology and pathophysiology of assisted reproduction before the first success in IVF, while the data supporting or refuting this hypothesis were less than conclusive. Thanks to sequencing data from the 16S rRNA subunit, we characterized the microbiome in the reproductive tract of infertile women, and we found that changes in the vaginal microbiome are related to female infertility. We also found that the characteristic microbiome bacteria are mainly members of several genera and that the vaginal microbiome of infertile women is not sensitive to hormonal changes during IVF. In conclusion, our report provides data that can be used for discovering the role of the vaginal microbiome in patients suffering from secondary infertility.
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23
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Wan H, Liu T, Su C, Ji X, Wang L, Zhao Y, Wang Z. Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1448-1457. [PMID: 31756265 DOI: 10.1002/jsfa.10151] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/28/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Baixi sufu (BS) is a traditional Chinese spicy fermented bean curd manufactured with a natural starter. In this study, the bacterial and fungal communities during BS fermentation were determined by culture and by the culture-independent method of high-throughput sequencing (HTS). Correlation analyses were performed to select the microorganisms potentially contributing to this fermentation. RESULTS During the fermentation of BS, 162 bacterial and 97 fungal strains were isolated and identified, and a total of 268 314 bacterial and 287 844 fungal high-quality sequences were analyzed. In general, lactic acid bacteria (LAB), especially Enterococcus and Lactococcus, were dominant in the early stage of fermentation, and spore-forming bacteria, especially Bacillus spp., became the predominant bacteria by the end of fermentation. Geotrichum, Mortierella, and unclassified Ascomycota, were the major fungal populations, which could not be detected in the final product. Correlation analyses indicated that Enterococcus, Bacillus, Geotrichum, and unclassified Ascomycota correlated significantly and positively with amino nitrogen. However, due to the sporulation characteristics of Bacillus, they may have little effect on BS ripening. The presence of Bifidobacterium spp. in sufu is reported for the first time, but the excessive counts of the Bacillus cereus group (>105 CFU g-1 ) indicate a potential hazard to consumers. CONCLUSION The profiles obtained from this study will contribute to the development of autochthonous starter cultures to control BS fermentation, and may lead to the development of novel strategies to shorten the fermentation time of sufu products. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Hongfang Wan
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Ting Liu
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Caiwei Su
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Xu Ji
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Liping Wang
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai, China
| | - Yong Zhao
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - Zhengquan Wang
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
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24
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Introduction of NGS in Environmental Surveillance for Healthcare-Associated Infection Control. Microorganisms 2019; 7:microorganisms7120708. [PMID: 31888282 PMCID: PMC6956231 DOI: 10.3390/microorganisms7120708] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 01/24/2023] Open
Abstract
The hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care. The monitoring of hospital surfaces is generally addressed by microbial cultural isolation, with some performance limitations. Hence there is need to implement environmental surveillance systems using more effective methods. This study aimed to evaluate next-generation sequencing (NGS) technologies for hospital environment microbiome characterization, in comparison with conventional and molecular methods, in an Italian pediatric hospital. Environmental samples included critical surfaces of randomized rooms, surgical rooms, intensive care units and delivery rooms. The resistome of the contaminating population was also evaluated. NGS, compared to other methods, detected with higher sensitivity the environmental bacteria, and was the only method able to detect even unsearched bacteria. By contrast, however, it did not detect mycetes, nor it could distinguish viable from dead bacteria. Microbiological and PCR methods could identify and quantify mycetes, in addition to bacteria, and PCR could define the population resistome. These data suggest that NGS could be an effective method for hospital environment monitoring, especially if flanked by PCR for species identification and resistome characterization, providing a potential tool for the control of HAI transmission.
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25
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Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR, MacIntyre DA. The association between vaginal bacterial composition and miscarriage: a nested case-control study. BJOG 2019; 127:264-274. [PMID: 31573753 PMCID: PMC6972675 DOI: 10.1111/1471-0528.15972] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/31/2023]
Abstract
Objective To characterise vaginal bacterial composition in early pregnancy and investigate its relationship with first and second trimester miscarriages. Design Nested case–control study. Setting Queen Charlotte’s and Chelsea Hospital, Imperial College Healthcare NHS Trust, London. Population 161 pregnancies: 64 resulting in first trimester miscarriage, 14 in second trimester miscarriage and 83 term pregnancies. Methods Prospective profiling and comparison of vaginal bacteria composition using 16S rRNA gene‐based metataxonomics from 5 weeks’ gestation in pregnancies ending in miscarriage or uncomplicated term deliveries matched for age, gestation and body mass index. Main outcome measures Relative vaginal bacteria abundance, diversity and richness. Pregnancy outcomes defined as first or second trimester miscarriage, or uncomplicated term delivery. Results First trimester miscarriage associated with reduced prevalence of Lactobacillus spp.‐dominated vaginal microbiota classified using hierarchical clustering analysis (65.6 versus 87.7%; P = 0.005), higher alpha diversity (mean Inverse Simpson Index 2.5 [95% confidence interval 1.8–3.0] versus 1.5 [1.3–1.7], P = 0.003) and higher richness 25.1 (18.5–31.7) versus 16.7 (13.4–20), P = 0.017), compared with viable pregnancies. This was independent of vaginal bleeding and observable before first trimester miscarriage diagnosis (P = 0.015). Incomplete/complete miscarriage associated with higher proportions of Lactobacillus spp.‐depleted communities compared with missed miscarriage. Early pregnancy vaginal bacterial stability was similar between miscarriage and term pregnancies. Conclusions These findings associate the bacterial component of vaginal microbiota with first trimester miscarriage and indicate suboptimal community composition is established in early pregnancy. While further studies are required to elucidate the mechanism, vaginal bacterial composition may represent a modifiable risk factor for first trimester miscarriage. Tweetable abstract Vaginal bacterial composition in first trimester miscarriage is associated with reduced Lactobacillus spp. abundance and is independent of vaginal bleeding. Vaginal bacterial composition in first trimester miscarriage is associated with reduced Lactobacillus spp. abundance and is independent of vaginal bleeding.
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Affiliation(s)
- M Al-Memar
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - S Bobdiwala
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - H Fourie
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - R Mannino
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Y S Lee
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK.,March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - A Smith
- School of Medicine, Cardiff University, Cardiff, UK
| | - J R Marchesi
- March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK.,Division of Integrative Systems Medicine and Digestive Disease, Imperial College London, London, UK.,School of Biosciences, Cardiff University, Cardiff, UK
| | - D Timmerman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - T Bourne
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK.,Department of Obstetrics and Gynaecology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - P R Bennett
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK.,March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - D A MacIntyre
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.,Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK.,March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
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26
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Campisciano G, Toschetti A, Comar M, Taranto RD, Berton F, Stacchi C. Shifts of subgingival bacterial population after nonsurgical and pharmacological therapy of localized aggressive periodontitis, followed for 1 year by Ion Torrent PGM platform. Eur J Dent 2019; 11:126-129. [PMID: 28435379 PMCID: PMC5379826 DOI: 10.4103/ejd.ejd_309_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The possibility of targeting the hypervariable region V3 of the 16S rRNA gene using Ion Torrent Personal Genome Machine (PGM) could provide a complete analysis of subgingival plaque samples, potentially able to identify microbiological species missed by culture-based methods. A 16-year-old female smoker patient, affected by localized aggressive periodontitis, underwent a full-mouth disinfection protocol and was inserted in a 3-month recall program. Microbiological samples were collected at baseline and at 30, 100, 365 days follow-up and analyzed by Ion Torrent PGM. Capnocytophaga, Fusobacterium, Prevotella, and Treponema were the most represented pathogens at baseline. Nonsurgical treatment and systemic antibiotics drastically lowered the anaerobic species, and their presence remained limited after 100 days, while a consistent recolonization by anaerobic bacteria was detected at 365 days. The patient showed a general improvement of periodontal conditions. Differently from polymerase chain reaction and other microarray techniques, Ion Torrent performs a quantitative analysis of the microbiota, irrespective of the searched species. An accurate definition of the shifts of the bacterial community might help periodontal researchers for a better understanding of the impact of different treatment approaches or in intercepting nonresponsive conditions.
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Affiliation(s)
- Giuseppina Campisciano
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Advanced Diagnostics Department, Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | | | - Manola Comar
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Advanced Diagnostics Department, Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | | | - Federico Berton
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Claudio Stacchi
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
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27
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Mu X, Zhao C, Yang J, Wei X, Zhang J, Liang C, Gai Z, Zhang C, Zhu D, Wang Y, Zhang L. Group B Streptococcus colonization induces Prevotella and Megasphaera abundance-featured vaginal microbiome compositional change in non-pregnant women. PeerJ 2019; 7:e7474. [PMID: 31440433 PMCID: PMC6699484 DOI: 10.7717/peerj.7474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Background Previous studies have indicated that variations in the vaginal microbiome result in symptomatic conditions. Group B Streptococcus (GBS) is a significant neonatal pathogen and maternal vaginal colonization has been recognized as an important risk factor for neonatal disease. Therefore, it is important to discover the relationship between the composition of the vaginal microbiome and GBS colonization. This study explores the potential relationship between the composition of the vaginal microbiome and GBS colonization in non-pregnant Chinese women. Methods A total of 22 GBS-positive, non-pregnant women and 44 matched GBS-negative women were recruited for the current study. The composition of the vaginal microbiome was profiled by sequencing the 16S rRNA genes. The microbiome diversity and variation were then evaluated. Results The vaginal microbiome of the 66 subjects enrolled in the current study were compared and the results showed that GBS-positive women exhibited significant vaginal microbial differences compared with the GBS-negative women based on the analysis of similarities (r = 0.306, p < 0.01). The relative abundance of the bacterial genus Lactobacillus (p < 0.01) was significantly lower in the GBS-positive group, while the abundances of the bacterial genera Prevotella (p < 0.01), Megasphaera (p < 0.01), and Streptococcus (p < 0.01) were significantly higher in the GBS-positive group. Discussion The current study addressed significant variations across the communities of the vaginal microbiome in GBS-positive and GBS-negative women in a Chinese cohort, which paves the way for a larger cohort-based clinical validation study and the development of therapeutic probiotics in the future.
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Affiliation(s)
- Xiaofeng Mu
- Tianjin University, Academy of Medical Engineering and Translational Medicine, Tianjin, China.,Clinical Laboratory and Core Research Laboratory; Qingdao Human Microbiome Center & Qingdao Institute of Oncology, The Affiliated Central Hospital of Qingdao University, Qingdao, China.,School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Changying Zhao
- Shandong Children's Microbiome Center, Qilu Children's Hospital of Shandong University, Jinan, China.,Research Institute of Pediatrics, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Junjie Yang
- College of Life Science, Qilu Normal University, Jinan, China
| | - Xiaofang Wei
- Clinical Laboratory and Core Research Laboratory; Qingdao Human Microbiome Center & Qingdao Institute of Oncology, The Affiliated Central Hospital of Qingdao University, Qingdao, China
| | - Jiaming Zhang
- School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Cheng Liang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Zhongtao Gai
- Shandong Children's Microbiome Center, Qilu Children's Hospital of Shandong University, Jinan, China.,Research Institute of Pediatrics, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Chunling Zhang
- Clinical Laboratory and Core Research Laboratory; Qingdao Human Microbiome Center & Qingdao Institute of Oncology, The Affiliated Central Hospital of Qingdao University, Qingdao, China
| | - Dequan Zhu
- Microbiological Laboratory; Department of Infection Management; Department of Neurosurgery, Lin Yi People's Hospital, Linyi, China
| | - Ye Wang
- Clinical Laboratory and Core Research Laboratory; Qingdao Human Microbiome Center & Qingdao Institute of Oncology, The Affiliated Central Hospital of Qingdao University, Qingdao, China
| | - Lei Zhang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China
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28
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A supersensitive MSPQC bacterium sensor based on 16S rRNA and “DNA-RNA switch”. Biosens Bioelectron 2019; 138:111302. [DOI: 10.1016/j.bios.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022]
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29
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Gommers LMM, Ederveen THA, van der Wijst J, Overmars-Bos C, Kortman GAM, Boekhorst J, Bindels RJM, de Baaij JHF, Hoenderop JGJ. Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia. FASEB J 2019; 33:11235-11246. [PMID: 31299175 DOI: 10.1096/fj.201900839r] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proton pump inhibitors (PPIs) are used by millions of patients for the treatment of stomach acid-reflux diseases. Although PPIs are generally considered safe, about 13% of the users develop hypomagnesemia. Despite rising attention for this issue, the underlying mechanism is still unknown. Here, we examine whether the gut microbiome is involved in the development of PPI-induced hypomagnesemia in wild-type C57BL/6J mice. After 4 wk of treatment under normal or low dietary Mg2+ availability, omeprazole significantly reduced serum Mg2+ levels only in mice on a low-Mg2+ diet without affecting the mRNA expression of colonic or renal Mg2+ transporters. Overall, 16S rRNA gene sequencing revealed a lower gut microbial diversity in omeprazole-treated mice. Omeprazole induced a shift in microbial composition, which was associated with a 3- and 2-fold increase in the abundance of Lactobacillus and Bifidobacterium, respectively. To examine the metabolic consequences of these microbial alterations, the colonic composition of organic acids was evaluated. Low dietary Mg2+ intake, independent of omeprazole treatment, resulted in a 10-fold increase in formate levels. Together, these results imply that both omeprazole treatment and low dietary Mg2+ intake disturb the gut internal milieu and may pose a risk for the malabsorption of Mg2+ in the colon.-Gommers, L. M. M., Ederveen, T. H. A., van der Wijst, J., Overmars-Bos, C., Kortman, G. A. M., Boekhorst, J., Bindels, R. J. M., de Baaij, J. H. F., Hoenderop, J. G. J. Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia.
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Affiliation(s)
- Lisanne M M Gommers
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,NIZO Food Research, Ede, The Netherlands
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Caro Overmars-Bos
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | | | - Jos Boekhorst
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,NIZO Food Research, Ede, The Netherlands
| | - René J M Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Jeroen H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
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30
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Meola M, Rifa E, Shani N, Delbès C, Berthoud H, Chassard C. DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products. BMC Genomics 2019; 20:560. [PMID: 31286860 PMCID: PMC6615214 DOI: 10.1186/s12864-019-5914-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Background Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation. Results We provide a manually curated database composed of 10’290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products. Electronic supplementary material The online version of this article (10.1186/s12864-019-5914-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Meola
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, Bern, 3003, Switzerland.
| | - Etienne Rifa
- Université Clermont Auvergne, INRA, VetAgro Sup, UMRF, 20 côte de Reyne, Aurillac, 15000, France
| | - Noam Shani
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, Bern, 3003, Switzerland
| | - Céline Delbès
- Université Clermont Auvergne, INRA, VetAgro Sup, UMRF, 20 côte de Reyne, Aurillac, 15000, France
| | - Hélène Berthoud
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, Bern, 3003, Switzerland
| | - Christophe Chassard
- Université Clermont Auvergne, INRA, VetAgro Sup, UMRF, 20 côte de Reyne, Aurillac, 15000, France
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Diaz PI, Hong BY, Dupuy AK, Choquette L, Thompson A, Salner AL, Schauer PK, Hegde U, Burleson JA, Strausbaugh LD, Peterson DE, Dongari-Bagtzoglou A. Integrated Analysis of Clinical and Microbiome Risk Factors Associated with the Development of Oral Candidiasis during Cancer Chemotherapy. J Fungi (Basel) 2019; 5:jof5020049. [PMID: 31200520 PMCID: PMC6617088 DOI: 10.3390/jof5020049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
Oral candidiasis is a common side effect of cancer chemotherapy. To better understand predisposing factors, we followed forty-five subjects who received 5-fluorouracil- or doxorubicin-based treatment, during one chemotherapy cycle. Subjects were evaluated at baseline, prior to the first infusion, and at three additional visits within a two-week window. We assessed the demographic, medical and oral health parameters, neutrophil surveillance, and characterized the salivary bacteriome and mycobiome communities through amplicon high throughput sequencing. Twenty percent of all subjects developed oral candidiasis. Using multivariate statistics, we identified smoking, amount of dental plaque, low bacteriome and mycobiome alpha-diversity, and the proportions of specific bacterial and fungal taxa as baseline predictors of oral candidiasis development during the treatment cycle. All subjects who developed oral candidiasis had baseline microbiome communities dominated by Candida and enriched in aciduric bacteria. Longitudinally, oral candidiasis was associated with a decrease in salivary flow prior to lesion development, and occurred simultaneously or before oral mucositis. Candidiasis was also longitudinally associated with a decrease in peripheral neutrophils but increased the neutrophil killing capacity of Candida albicans. Oral candidiasis was not found to be associated with mycobiome structure shifts during the cycle but was the result of an increase in Candida load, with C. albicans and Candida dubliniensis being the most abundant species comprising the salivary mycobiome of the affected subjects. In conclusion, we identified a set of clinical and microbiome baseline factors associated with susceptibility to oral candidiasis, which might be useful tools in identifying at risk individuals, prior to chemotherapy.
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Affiliation(s)
- Patricia I Diaz
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT 06030, USA.
| | - Bo-Young Hong
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT 06030, USA.
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Amanda K Dupuy
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Linda Choquette
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT 06030, USA.
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Angela Thompson
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT 06030, USA.
| | - Andrew L Salner
- Department of Medical Oncology, Hartford Healthcare, Hartford, CT 06106, USA.
| | - Peter K Schauer
- Department of Medical Oncology, Hartford Healthcare, Hartford, CT 06106, USA.
| | - Upendra Hegde
- Department of Medicine, UConn Health, Farmington, CT 06030, USA.
| | - Joseph A Burleson
- Department of Community Medicine and Health Care, UConn Health, Farmington, CT 06032, USA.
| | - Linda D Strausbaugh
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Douglas E Peterson
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT 06030, USA.
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT 06030, USA.
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Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR, MacIntyre DA. Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes. Transl Res 2019; 207:30-43. [PMID: 30633889 PMCID: PMC6489901 DOI: 10.1016/j.trsl.2018.12.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 10/31/2022]
Abstract
Vaginal bacterial community composition influences pregnancy outcome. Preterm prelabor rupture of the fetal membranes (PPROM), which precedes 30% of all spontaneous preterm births, is associated with high vaginal bacterial diversity prior to rupture. The point at which vaginal bacterial diversity is established before PPROM is unknown. In this study, we use metataxonomics to longitudinally characterize the vaginal bacterial composition from as early as 6 weeks of gestation in women at high (n = 38) and low (n = 22) risk of preterm birth who subsequently experience PPROM and in women delivering at term without complications (n = 36). Reduced Lactobacillus spp. abundance and high diversity was observed prior to PPROM in 20% and 26% of women at low and high risk of preterm births respectively, but in only 3% of women who delivered at term. PPROM was associated with instability of bacterial community structure during pregnancy and a shift toward higher diversity predominately occurring during the second trimester. This was characterized by increased relative abundance of potentially pathogenic species including Prevotella, Peptoniphilus, Streptococcus, and Dialister. This study identifies reduced Lactobacillus spp. abundance and increasing vaginal bacterial diversity as an early risk factor for PPROM and highlights the need for interventional studies designed to assess the impact of modifying vaginal bacterial composition for the prevention of preterm birth.
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Key Words
- bmi, body mass index
- dna, deoxyribonucleic acid
- ena, european nucleotide archive
- ga, gestational age
- hca, hierarchical cluster analysis
- lda, latent discriminatory analysis
- mr, membrane rupture
- nhs, national health service
- nice, national institute for health and care excellence
- pcr, polymerase chain reaction
- pprom, preterm prelabor rupture of the fetal membranes
- ptb, preterm birth
- rdp, ribosomal database project
- sra, sequence read archive
- stamp, statistical analysis of metagenomic profiles
- sop, standard operating procedure
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Affiliation(s)
- Richard G Brown
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Maya Al-Memar
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Julian R Marchesi
- March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK; Centre for Digestive and Gut Health, Imperial College London, London, UK; School of Biosciences, Cardiff University, Cardiff, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - Ann Smith
- School of Medicine, Cardiff University, Cardiff, UK
| | - Denise Chan
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Holly Lewis
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Lindsay Kindinger
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Vasso Terzidou
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK; Chelsea & Westminster Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Tom Bourne
- March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes European Preterm Birth Research Centre, Imperial College London, London, UK.
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Hong BY, Sobue T, Choquette L, Dupuy AK, Thompson A, Burleson JA, Salner AL, Schauer PK, Joshi P, Fox E, Shin DG, Weinstock GM, Strausbaugh LD, Dongari-Bagtzoglou A, Peterson DE, Diaz PI. Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis. MICROBIOME 2019; 7:66. [PMID: 31018870 PMCID: PMC6482518 DOI: 10.1186/s40168-019-0679-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/02/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes the primary injury trigger, the interaction of oral microbial commensals with mucosal tissues could modify the response. It is not clear, however, whether chemotherapy and its associated treatments affect oral microbial communities disrupting the homeostatic balance between resident microorganisms and the adjacent mucosa and if such alterations are associated with mucositis. To gain knowledge on the pathophysiology of oral mucositis, 49 subjects receiving 5-fluorouracil (5-FU) or doxorubicin-based chemotherapy were evaluated longitudinally during one cycle, assessing clinical outcomes, bacterial and fungal oral microbiome changes, and epithelial transcriptome responses. As a control for microbiome stability, 30 non-cancer subjects were longitudinally assessed. Through complementary in vitro assays, we also evaluated the antibacterial potential of 5-FU on oral microorganisms and the interaction of commensals with oral epithelial tissues. RESULTS Oral mucositis severity was associated with 5-FU, increased salivary flow, and higher oral granulocyte counts. The oral bacteriome was disrupted during chemotherapy and while antibiotic and acid inhibitor intake contributed to these changes, bacteriome disruptions were also correlated with antineoplastics and independently and strongly associated with oral mucositis severity. Mucositis-associated bacteriome shifts included depletion of common health-associated commensals from the genera Streptococcus, Actinomyces, Gemella, Granulicatella, and Veillonella and enrichment of Gram-negative bacteria such as Fusobacterium nucleatum and Prevotella oris. Shifts could not be explained by a direct antibacterial effect of 5-FU, but rather resembled the inflammation-associated dysbiotic shifts seen in other oral conditions. Epithelial transcriptional responses during chemotherapy included upregulation of genes involved in innate immunity and apoptosis. Using a multilayer epithelial construct, we show mucositis-associated dysbiotic shifts may contribute to aggravate mucosal damage since the mucositis-depleted Streptococcus salivarius was tolerated as a commensal, while the mucositis-enriched F. nucleatum displayed pro-inflammatory and pro-apoptotic capacity. CONCLUSIONS Altogether, our work reveals that chemotherapy-induced oral mucositis is associated with bacterial dysbiosis and demonstrates the potential for dysbiotic shifts to aggravate antineoplastic-induced epithelial injury. These findings suggest that control of oral bacterial dysbiosis could represent a novel preventive approach to ameliorate oral mucositis.
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Affiliation(s)
- Bo-Young Hong
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Takanori Sobue
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
| | - Linda Choquette
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Amanda K Dupuy
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Angela Thompson
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
| | - Joseph A Burleson
- Department of Community Medicine and Health Care, UConn Health, Farmington, CT, USA
| | | | | | - Pujan Joshi
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Evan Fox
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
| | - Dong-Guk Shin
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | | | - Linda D Strausbaugh
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
| | - Douglas E Peterson
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA
| | - Patricia I Diaz
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
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Palmer RJ, Cotton SL, Kokaras AS, Gardner P, Grisius M, Pelayo E, Warner B, Paster BJ, Alevizos I. Analysis of oral bacterial communities: comparison of HOMI NGS with a tree-based approach implemented in QIIME. J Oral Microbiol 2019; 11:1586413. [PMID: 30988892 PMCID: PMC6450576 DOI: 10.1080/20002297.2019.1586413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/19/2019] [Accepted: 01/28/2019] [Indexed: 01/09/2023] Open
Abstract
Background: Molecular taxonomic assignments in oral microbial communities have been made using probe-matching approaches, but never compared to those obtained by more readily accepted tree-based approaches. Objective: To compare community composition profiles obtained from a probe-matching approach (HOMINGS) to those from a closed-ended tree-based approach (QIIME using the eHOMD database). Design: HOMINGS and QIIME were used for parallel analysis of ten mock community samples, and of 119 supragingival plaque samples from ecologically unique sites (sound tooth surfaces in healthy subjects, sound tooth surfaces in patients with primary Sjögren’s Syndrome, and carious lesions in Sjögren’s Syndrome patients). Linear discriminant analysis Effective Size (LEfSe) was used to identify discriminating taxa among the natural plaque samples. Results: Community composition profiles of all samples were congruent between the two analysis aproaches. Alpha and beta diversity of the natural plaque communities were likewise similar. Communities from pSS patients and those from individuals with normal salivary flow differed in alpha and beta diversity. Both classification approaches yielded differences in composition predicted for samples from these subject cohorts, and discriminating taxa were similar between approaches. Conclusions: A direct comparison demonstrates that HOMINGS is largely equivalent to the tree-based approach as implemented here.
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Affiliation(s)
- Robert J Palmer
- Oral Immunity and Inflammation Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Sean L Cotton
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Alexis S Kokaras
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Pamela Gardner
- Sjögren's Syndrome Clinic, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Margaret Grisius
- Sjögren's Syndrome Clinic, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Eileen Pelayo
- Sjögren's Syndrome Clinic, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Blake Warner
- Sjögren's Syndrome Clinic, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.,AAV Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Bruce J Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Ilias Alevizos
- Sjögren's Syndrome Clinic, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.,Salivary Gland Dysfunction Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
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35
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Yilmaz B, Juillerat P, Øyås O, Ramon C, Bravo FD, Franc Y, Fournier N, Michetti P, Mueller C, Geuking M, Pittet VEH, Maillard MH, Rogler G, Wiest R, Stelling J, Macpherson AJ. Microbial network disturbances in relapsing refractory Crohn's disease. Nat Med 2019; 25:323-336. [PMID: 30664783 DOI: 10.1038/s41591-018-0308-z] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD) can be broadly divided into Crohn's disease (CD) and ulcerative colitis (UC) from their clinical phenotypes. Over 150 host susceptibility genes have been described, although most overlap between CD, UC and their subtypes, and they do not adequately account for the overall incidence or the highly variable severity of disease. Replicating key findings between two long-term IBD cohorts, we have defined distinct networks of taxa associations within intestinal biopsies of CD and UC patients. Disturbances in an association network containing taxa of the Lachnospiraceae and Ruminococcaceae families, typically producing short chain fatty acids, characterize frequently relapsing disease and poor responses to treatment with anti-TNF-α therapeutic antibodies. Alterations of taxa within this network also characterize risk of later disease recurrence of patients in remission after the active inflamed segment of CD has been surgically removed.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pascal Juillerat
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ove Øyås
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Charlotte Ramon
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Francisco Damian Bravo
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yannick Franc
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Nicolas Fournier
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Pierre Michetti
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Christoph Mueller
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Markus Geuking
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Valerie E H Pittet
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Michel H Maillard
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Reiner Wiest
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland. .,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.
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36
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McGee KM, Eaton WD, Shokralla S, Hajibabaei M. Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area. MICROBIAL ECOLOGY 2019; 77:148-167. [PMID: 29858646 DOI: 10.1007/s00248-018-1206-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (Cmic); NO3-; NH4+; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil Cmic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil Cmic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil Cmic and soil fungal community structure were significantly related to levels of soil NO3-. Our analyses showed that even after 33 years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil Cmic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil Cmic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.
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Affiliation(s)
- Katie M McGee
- Centre for Biodiversity Genomics at Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - William D Eaton
- Department of Biology, Pace University, 1 Pace Plaza, New York, NY, 10038, USA
| | - Shadi Shokralla
- Centre for Biodiversity Genomics at Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics at Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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Molecular Characterization of Aniline Biodegradation by Some Bacterial Isolates having Unexpressed Catechol 2,3-Dioxygenase Gene. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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38
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Farrell MJ, Govender D, Hajibabaei M, van der Bank M, Davies TJ. Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach 1. Genome 2018; 62:229-242. [PMID: 30495980 DOI: 10.1139/gen-2018-0064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteria are essential components of natural environments. They contribute to ecosystem functioning through roles as mutualists and pathogens for larger species, and as key components of food webs and nutrient cycles. Bacterial communities respond to environmental disturbances, and the tracking of these communities across space and time may serve as indicators of ecosystem health in areas of conservation concern. Recent advances in DNA sequencing of environmental samples allow for rapid and culture-free characterization of bacterial communities. Here we conduct the first metabarcoding survey of bacterial diversity in the waterholes of the Kruger National Park, South Africa. We show that eDNA can be amplified from waterholes and find strongly structured microbial communities, likely reflecting local abiotic conditions, animal ecology, and anthropogenic disturbance. Over timescales from days to weeks we find increased turnover in community composition, indicating bacteria may represent host-associated taxa of large vertebrates visiting the waterholes. Through taxonomic annotation we also identify pathogenic taxa, demonstrating the utility of eDNA metabarcoding for surveillance of infectious diseases. These samples serve as a baseline survey of bacterial diversity in the Kruger National Park, and in the future, spatially distinct microbial communities may be used as markers of ecosystem disturbance, or biotic homogenization across the park.
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Affiliation(s)
- Maxwell J Farrell
- a Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal, QC H3A 0G4, Québec, Canada
| | - Danny Govender
- b Scientific Services, Kruger National Park, SANParks, Private Bag X402, Skukuza, 1350, South Africa.,c Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - Mehrdad Hajibabaei
- d Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Michelle van der Bank
- e African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, Johannesburg, South Africa
| | - T Jonathan Davies
- e African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, Johannesburg, South Africa.,f Botany, Forest & Conservation Sciences, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
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Ghosh A, Bhadury P. Exploring biogeographic patterns of bacterioplankton communities across global estuaries. Microbiologyopen 2018; 8:e00741. [PMID: 30303297 PMCID: PMC6528645 DOI: 10.1002/mbo3.741] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022] Open
Abstract
Estuaries provide an ideal niche to study structure and function of bacterioplankton communities owing to the presence of a multitude of environmental stressors. Bacterioplankton community structures from nine global estuaries were compared to understand their broad‐scale biogeographic patterns. Bacterioplankton community structure from four estuaries of Sundarbans, namely Mooriganga, Thakuran, Matla, and Harinbhanga, was elucidated using Illumina sequencing. Bacterioplankton communities from these estuaries were compared against available bacterioplankton sequence data from Columbia, Delaware, Jiulong, Pearl, and Hangzhou estuaries. All nine estuaries were dominated by Proteobacteria. Other abundant phyla included Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Verrucomicrobia. The abundant bacterial phyla showed a ubiquitous presence across the estuaries. At class level, the overwhelming abundance of Gammaproteobacteria in the estuaries of Sundarbans and Columbia estuary clearly stood out amidst high abundance of Alphaproteobacteria observed in the other estuaries. Abundant bacterial families including Rhodobacteriaceae, Shingomonadaceae, Acidobacteriaceae, Vibrionaceae, and Xanthomondaceae also showed ubiquitous presence in the studied estuaries. However, rare taxa including Chloroflexi, Tenericutes, Nitrospirae, and Deinococcus‐Thermus showed clear site‐specific distribution patterns. Such distribution patterns were also reinstated by nMDS ordination plots. Such clustering patterns could hint toward the potential role of environmental parameters and substrate specificity which could result in distinct bacterioplankton communities at specific sites. The ubiquitous presence of abundant bacterioplankton groups along with their strong correlation with surface water temperature and dissolved nutrient concentrations indicates the role of such environmental parameters in shaping bacterioplankton community structure in estuaries. Overall, studies on biogeographic patters of bacterioplankton communities can provide interesting insights into ecosystem functioning and health of global estuaries.
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Affiliation(s)
- Anwesha Ghosh
- Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
| | - Punyasloke Bhadury
- Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India
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40
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Dong L, Yin J, Zhao J, Ma SR, Wang HR, Wang M, Chen W, Wei WQ. Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus. Front Microbiol 2018; 9:1603. [PMID: 30065718 PMCID: PMC6056649 DOI: 10.3389/fmicb.2018.01603] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/11/2022] Open
Abstract
Human microbial communities are highly complex ecosystems, but it remains unclear if microbial compositions have any similarity in distinct sites of the oral cavity and esophagus in particular. Clinical samples were collected from three niches (saliva, tongue dorsum and supragingival plaque) of the oral cavity and three segments (upper, middle, and lower) of the esophagus in 27 healthy individuals. Bacterial V3-V4 region of 16S rRNA gene in these samples was amplified and sequenced on Illumina sequencing platform, followed by data analysis using QIIME and LEfSe softwares. Highly diverse bacterial flora with 365 genera belonging to 29 phyla resided in the oral cavity and 594 genera belonging to 29 phyla in the esophagus. The phyla Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and TM7 were most abundant in both the oral cavity and the esophagus, but the phyla Actinobacteria and Bacteroidetes were preferable in the oral cavity and Firmicutes in the esophagus. The genera Streptococcus, Neisseria, Prevotella, Actinobacillus, and Veillonella were most abundant in both oral cavity and esophagus, but Neisseria was preferable in the oral cavity and Streptococcus in the esophagus. Different niche-specific bacterial signatures were found in the oral cavity, e.g., the class Flavobacteria in the supragingival plaque, class Bacteroides in the saliva and the class Clostridia in the tongue dorsum. By contrast, no site specific bacteria for three different segments of esophagus were found. However, high variability of microbial compositions between individuals was observed. In conclusion, this study confirmed microbial diversity at different taxonomic levels in healthy oral cavity and esophagus, and identified the site-preferable bacterial signatures in six niches of the upper digestive tract. These findings provide a critical baseline for future studies interpreting microbiome-related diseases.
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Affiliation(s)
- Li Dong
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jian Yin
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhao
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shan-Rui Ma
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Rui Wang
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Wang
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Chen
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen-Qiang Wei
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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41
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Nakano M. 16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products. J Food Prot 2018; 81:848-859. [PMID: 29664320 DOI: 10.4315/0362-028x.jfp-17-346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.
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Affiliation(s)
- Miyo Nakano
- Division of Food Science, Toyo Institute of Food Technology, 23-2, 4-chome, Minami-hanayashiki, Kawanishi-shi, Hyogo, 666-0026 Japan
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42
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McAllister T, Dunière L, Drouin P, Xu S, Wang Y, Munns K, Zaheer R. Silage review: Using molecular approaches to define the microbial ecology of silage. J Dairy Sci 2018; 101:4060-4074. [DOI: 10.3168/jds.2017-13704] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/21/2017] [Indexed: 12/11/2022]
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43
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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44
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Girard-Madoux MJ, Gomez de Agüero M, Ganal-Vonarburg SC, Mooser C, Belz GT, Macpherson AJ, Vivier E. The immunological functions of the Appendix: An example of redundancy? Semin Immunol 2018; 36:31-44. [DOI: 10.1016/j.smim.2018.02.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/16/2018] [Indexed: 12/12/2022]
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45
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Porter TM, Hajibabaei M. Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol Ecol 2018; 27:313-338. [PMID: 29292539 DOI: 10.1111/mec.14478] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 12/19/2022]
Abstract
The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.
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Affiliation(s)
- Teresita M Porter
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.,Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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46
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Campisciano G, Zanotta N, Licastro D, De Seta F, Comar M. In vivo microbiome and associated immune markers: New insights into the pathogenesis of vaginal dysbiosis. Sci Rep 2018; 8:2307. [PMID: 29396486 PMCID: PMC5797242 DOI: 10.1038/s41598-018-20649-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/23/2018] [Indexed: 02/03/2023] Open
Abstract
The microbiota fulfils a key role in the training and function of the immune system, which contributes to the symbiosis between the host and complex microbial communities. In this study, we characterized the interplay between vaginal bacteria and local immune mediators during dysbiosis in selected women of reproductive age who were grouped according to Nugent’s criteria. The abundance of Gardnerella vaginalis and Bifidobacterium breve was increased in the intermediate dysbiotic status, while the presence of a plethora of non-resident bacteria characterized the group with overt vaginosis. In response to these increases, the anti-inflammatory IL1ra and pro-inflammatory IL2 increased, while the embryo trophic factors FGFβ and GMCSF decreased compared to the healthy milieu. A specific pattern, including IL1α, IL1β, IL8, MIG, MIP1α and RANTES, distinguished the intermediate group from the vaginosis group, while IL5 and IL13, which are secreted by Th2 cells, were significantly associated with the perturbation of the commensals Lactobacilli, Gardnerella and Ureaplasma. Summarizing, we postulate that although the dysbiotic condition triggers a pro-inflammatory process, the presence of a steady state level of Th2 may influence clinical manifestations. These results raise clinically relevant questions regarding the use of vaginal immunological markers as efficacious tools to monitor microbial alterations.
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Affiliation(s)
- Giuseppina Campisciano
- SSD of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy
| | - Nunzia Zanotta
- SSD of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy
| | - Danilo Licastro
- CBM Scrl-Genomics, Area Science Park, Basovizza, 34149, Trieste, Italy
| | - Francesco De Seta
- Medical Sciences Department, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy.,SC of Gynecology - Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy
| | - Manola Comar
- SSD of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy. .,Medical Sciences Department, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy.
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47
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Abstract
In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.
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48
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Brown RG, Marchesi JR, Lee YS, Smith A, Lehne B, Kindinger LM, Terzidou V, Holmes E, Nicholson JK, Bennett PR, MacIntyre DA. Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin. BMC Med 2018; 16:9. [PMID: 29361936 PMCID: PMC5782380 DOI: 10.1186/s12916-017-0999-x] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Preterm prelabour rupture of the fetal membranes (PPROM) precedes 30% of preterm births and is a risk factor for early onset neonatal sepsis. As PPROM is strongly associated with ascending vaginal infection, prophylactic antibiotics are widely used. The evolution of vaginal microbiota compositions associated with PPROM and the impact of antibiotics on bacterial compositions are unknown. METHODS We prospectively assessed vaginal microbiota prior to and following PPROM using MiSeq-based sequencing of 16S rRNA gene amplicons and examined the impact of erythromycin prophylaxis on bacterial load and community structures. RESULTS In contrast to pregnancies delivering at term, vaginal dysbiosis characterised by Lactobacillus spp. depletion was present prior to the rupture of fetal membranes in approximately a third of cases (0% vs. 27%, P = 0.026) and persisted following membrane rupture (31%, P = 0.005). Vaginal dysbiosis was exacerbated by erythromycin treatment (47%, P = 0.00009) particularly in women initially colonised by Lactobacillus spp. Lactobacillus depletion and increased relative abundance of Sneathia spp. were associated with subsequent funisitis and early onset neonatal sepsis. CONCLUSIONS Our data show that vaginal microbiota composition is a risk factor for subsequent PPROM and is associated with adverse short-term maternal and neonatal outcomes. This highlights vaginal microbiota as a potentially modifiable antenatal risk factor for PPROM and suggests that routine use of erythromycin for PPROM be re-examined.
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Affiliation(s)
- Richard G Brown
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Julian R Marchesi
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK.,School of Biosciences, Cardiff University, Cardiff, CF103AX, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Ann Smith
- School of Biosciences, Cardiff University, Cardiff, CF103AX, UK
| | - Benjamin Lehne
- Department of Epidemiology & Biostatistics, Medicine, Imperial College London, London, W2 1PG, UK
| | - Lindsay M Kindinger
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Vasso Terzidou
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.,Chelsea & Westminster Hospital, Imperial College Healthcare NHS Trust, London, SW10 9NH, UK
| | - Elaine Holmes
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK.,Division of Computational Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Jeremy K Nicholson
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK.,Division of Computational Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.,Queen Charlotte's Hospital, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK.
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49
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Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 996] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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50
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Li J, Fu R, Yang Y, Horz HP, Guan Y, Lu Y, Lou H, Tian L, Zheng S, Liu H, Shi M, Tang K, Wang S, Xu S. A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups. Syst Appl Microbiol 2017; 41:1-12. [PMID: 29129355 DOI: 10.1016/j.syapm.2017.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project. Systematic analysis of the gut communities in terms of their abundance and genetic composition was also performed, together with a genome-wide association study of the host genomes. The gut microbiota of 192 subjects was clearly classified into two enterotypes (Bacteroides and Prevotella). Interestingly, both enterotypes showed a clear genetic differentiation in terms of their functional catalogue of genes, especially for genes involved in amino acid and carbohydrate metabolism. In addition, several differentiated genera and genes were found among the three populations. Notably, one human variant (rs878394) was identified that showed significant association with the abundance of Prevotella, which is linked to LYPLAL1, a gene associated with body fat distribution, the waist-hip ratio and insulin sensitivity. Taken together, considerable differentiation was observed in gut microbes between enterotypes and among populations that was reflected in both the taxonomic composition and the genetic makeup of their functional genes, which could have been influenced by a variety of factors, such as diet and host genetic variation.
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Affiliation(s)
- Jing Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Ruiqing Fu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Yaqun Guan
- Department of Biochemistry, Preclinical Medicine College, XinJiang Medical University, Urumqi 830011, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Haiyi Lou
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Lei Tian
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Zheng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Hongjiao Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Meng Shi
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.
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