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Constante M, Libertucci J, Galipeau HJ, Szamosi JC, Rueda G, Miranda PM, Pinto-Sanchez MI, Southward CM, Rossi L, Fontes ME, Chirdo FG, Surette MG, Bercik P, Caminero A, Verdu EF. Biogeographic Variation and Functional Pathways of the Gut Microbiota in Celiac Disease. Gastroenterology 2022; 163:1351-1363.e15. [PMID: 35810781 DOI: 10.1053/j.gastro.2022.06.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/02/2022] [Accepted: 06/29/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND & AIMS Genes and gluten are necessary but insufficient to cause celiac disease (CeD). Altered gut microbiota has been implicated as an additional risk factor. Variability in sampling site may confound interpretation and mechanistic insight, as CeD primarily affects the small intestine. Thus, we characterized CeD microbiota along the duodenum and in feces and verified functional impact in gnotobiotic mice. METHODS We used 16S rRNA gene sequencing (Illumina) and predicted gene function (PICRUSt2) in duodenal biopsies (D1, D2 and D3), aspirates, and stool from patients with active CeD and controls. CeD alleles were determined in consented participants. A subset of duodenal samples stratified according to similar CeD risk genotypes (controls DQ2-/- or DQ2+/- and CeD DQ2+/-) were used for further analysis and to colonize germ-free mice for gluten metabolism studies. RESULTS Microbiota composition and predicted function in CeD was largely determined by intestinal location. In the duodenum, but not stool, there was higher abundance of Escherichia coli (D1), Prevotella salivae (D2), and Neisseria (D3) in CeD vs controls. Predicted bacterial protease and peptidase genes were altered in CeD and impaired gluten degradation was detected only in mice colonized with CeD microbiota. CONCLUSIONS Our results showed luminal and mucosal microbial niches along the gut in CeD. We identified novel microbial proteolytic pathways involved in gluten detoxification that are impaired in CeD but not in controls carrying DQ2, suggesting an association with active duodenal inflammation. Sampling site should be considered a confounding factor in microbiome studies in CeD.
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Affiliation(s)
- Marco Constante
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Josie Libertucci
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Heather J Galipeau
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Jake C Szamosi
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Gaston Rueda
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Pedro M Miranda
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Maria Ines Pinto-Sanchez
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Carolyn M Southward
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Laura Rossi
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Michelle E Fontes
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Fernando G Chirdo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Estudios Inmunológicos y Fisiopatológicos, Universidad Nacional de La Plata-National Scientific and Technical Research Council, La Plata, Argentina
| | - Michael G Surette
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Ontario, Canada
| | - Premysl Bercik
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Alberto Caminero
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
| | - Elena F Verdu
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
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Libertucci J, Constante M, Galipeau HJ, Szamosi JC, Rueda GH, Pinto-Sanchez MI, Southward CM, Rossi LM, Fontes ME, Chirdo FG, Surette M, Bercik P, CAMINERO FERNANDEZ A, Verdu E. A46 BIOGEOGRAPHIC VARIATION AND FUNCTIONAL PATHWAYS OF THE GUT MICROBIOTA IN CELIAC DISEASE. J Can Assoc Gastroenterol 2022. [PMCID: PMC8859172 DOI: 10.1093/jcag/gwab049.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Genes and gluten are necessary, but insufficient to cause celiac disease (CeD), as risk alleles (DQ2 or DQ8) are prevalent in ~30–40% of the healthy population consuming gluten. Gut microbiota shifts and infections have been proposed as risk modulators. Biogeographic characterization of the microbiota in CeD patients and its functional significance are limited, particularly at the duodenum, the main site of inflammation. Aims We studied microbiota composition and predicted function along the gastrointestinal tract and investigated the impact of host genetics and CeD activity. Methods We used 16S rRNA gene sequencing (Illumina) and predicted gene function analysis (PICRUSt2), to study the microbiota in duodenal biopsies (D1, D2 and D3), duodenal aspirates, and fecal samples from patients with active CeD (n= 24) (biopsy and serology confirmed) and controls (non-celiac, n= 41). CeD alleles were determined in consented participants using DQ-CD typing. Small intestinal samples from controls (DQ2-/- = 14; DQ2+/- = 7) and CeD (DQ2+/- = 12) were used for further analysis and to colonize C57BL/6 germ-free mice for gluten metabolism studies. Results Microbiota community composition and predicted function was mainly determined by intestinal location (P= 0.001). Within the duodenum, but not in stool, CeD patients had increased abundance of opportunistic pathogens. Escherichia coli was increased in D1, Streptococcus pneumoniae in D2, and Neisseria in D3 versus controls. Predicted bacterial protease and peptidase genes were altered in CeD DQ2+/- patients versus DQ2-/- controls. In DQ2+/- controls, fewer predicted bacterial genes were altered compared to CeD DQ2+/- patients. Impaired capacity to metabolize gluten was confirmed in germ-free mice colonized with microbiota from CeD (DQ2+/-), but not DQ2+/- or DQ2-/- controls. Conclusions In the duodenum, CeD is associated with increased opportunistic pathogens and altered bacterial proteolytic profile. These are not determined by genetic predisposition, as CeD and controls with similar genetic background differed in its predicted bacterial proteolytic function, which was confirmed in mice colonized with duodenal microbiota using these cohorts. Our study highlights the need for defining sampling location in studies investigating the role of microbiota in CeD. Funding Agencies CAG, CCC, CIHR
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Affiliation(s)
- J Libertucci
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - M Constante
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - H J Galipeau
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - J C Szamosi
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - G H Rueda
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - M I Pinto-Sanchez
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - C M Southward
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - L M Rossi
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - M E Fontes
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - F G Chirdo
- Universidad Nacional de la Plata, La Plata, Argentina
| | - M Surette
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - P Bercik
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | | | - E Verdu
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
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3
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Moossavi S, Fontes ME, Rossi L, Fusch G, Surette MG, Azad MB. Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study. FEMS Microbiol Lett 2021; 368:6070652. [PMID: 33417698 DOI: 10.1093/femsle/fnab001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimized and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for 2 weeks (short-term frozen). Long-term samples were stored at -20°C for >6 months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria, including Streptococcus, Staphylococcus and Bifidobacterium, from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.
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Affiliation(s)
- Shirin Moossavi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.,Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 14117-13135, Iran.,Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, AB T2N 4Z1, Canada
| | - Michelle E Fontes
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Laura Rossi
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Gerhard Fusch
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael G Surette
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Meghan B Azad
- Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
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Wang H, Kwon YH, Dewan V, Vahedi F, Syed S, Fontes ME, Ashkar AA, Surette MG, Khan WI. TLR2 Plays a Pivotal Role in Mediating Mucosal Serotonin Production in the Gut. J I 2019; 202:3041-3052. [DOI: 10.4049/jimmunol.1801034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/13/2019] [Indexed: 12/22/2022]
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Libertucci J, Dutta U, Kaur S, Jury J, Rossi L, Fontes ME, Shajib MS, Khan WI, Surette MG, Verdu EF, Armstrong D. Inflammation-related differences in mucosa-associated microbiota and intestinal barrier function in colonic Crohn's disease. Am J Physiol Gastrointest Liver Physiol 2018; 315:G420-G431. [PMID: 29848021 DOI: 10.1152/ajpgi.00411.2017] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Crohn's disease (CD), characterized by discontinuous intestinal injury and inflammation, has been associated with changes in luminal microbial composition and impaired barrier function. The relationships between visual features of intestinal injury, permeability, and the mucosa-associated microbiota are unclear. Individuals undergoing routine colonoscopy (controls) and patients with CD were evaluated by clinical parameters and confocal laser scanning endomicroscopic colonoscopy (CLE). Patients with CD were categorized as either CD with no injury (CD-NI) or CD with injury (CD-I). Colonic biopsies were taken from adjacent matched sites in all individuals, and CLE images from these sites were analyzed for vascular permeability. Microbial composition was evaluated by 16S rRNA gene sequencing of the V3 region, and the mycome was identified through internal transcribed spacer 2 sequencing. Subgroup analyses were performed for histology, paracellular permeability (Ussing chamber), and encroachment of bacteria (fluorescent in situ hybridization). CD-I patients showed an altered microbial community compared with both controls and CD-NI patients, with enrichment in Escherichia and a decrease in Firmicutes, including Lachnospira, Faecalibacterium, and Blautia. In CD-I patients, bacterial encroachment to host epithelial cells was greater in sites of injury than in matched biopsy sites. Biopsies from sites of injury also demonstrated greater vascular and paracellular permeability. Overall, CD-I patients showed an altered mucosal microbial community compared with CD-NI patients and controls. Matched biopsy samples in CD-I patients revealed that sites of injury, identified endoscopically, are characterized by increased encroachment of bacteria to host epithelial cells, associated with increased paracellular and vascular permeability, which may drive inflammation in CD. NEW & NOTEWORTHY Patients with Crohn's disease (CD) with areas of colonic injury have an altered microbial community compared with patients who have no endoscopic evidence of injury or active disease. Although matched biopsies from patients with colonic injury show no differences in the mucosa-associated microbiota, injured sites are associated with increased permeability and increased encroachment. Our results support the notion that dysbiotic communities within patients with colonic injury cause or permit disruption of the mucosal and endothelial layers in CD.
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Affiliation(s)
- Josie Libertucci
- Department of Biochemistry and Biomedical Sciences, McMaster University , Hamilton, Ontario , Canada.,Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada
| | - Usha Dutta
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research , Chandigarh , India
| | - Sandeep Kaur
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Medicine, McMaster University , Hamilton, Ontario , Canada
| | - Jennifer Jury
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Medicine, McMaster University , Hamilton, Ontario , Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University , Hamilton, Ontario , Canada.,Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada
| | - Michelle E Fontes
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Medicine, McMaster University , Hamilton, Ontario , Canada
| | - M Sharif Shajib
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Pathology and Molecular Medicine, McMaster University , Hamilton, Ontario , Canada
| | - Waliul I Khan
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Pathology and Molecular Medicine, McMaster University , Hamilton, Ontario , Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University , Hamilton, Ontario , Canada.,Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Medicine, McMaster University , Hamilton, Ontario , Canada
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Medicine, McMaster University , Hamilton, Ontario , Canada
| | - David Armstrong
- Farncombe Family Digestive Health Research Institute, McMaster University , Hamilton, Ontario , Canada.,Department of Medicine, McMaster University , Hamilton, Ontario , Canada
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Mendonca ML, Szamosi JC, Lacroix AM, Fontes ME, Bowdish DM, Surette MG. The sil Locus in Streptococcus Anginosus Group: Interspecies Competition and a Hotspot of Genetic Diversity. Front Microbiol 2017; 7:2156. [PMID: 28119678 PMCID: PMC5222867 DOI: 10.3389/fmicb.2016.02156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/21/2016] [Indexed: 01/09/2023] Open
Abstract
The Streptococcus Invasion Locus (Sil) was first described in Streptococcus pyogenes and Streptococcus pneumoniae, where it has been implicated in virulence. The two-component peptide signaling system consists of the SilA response regulator and SilB histidine kinase along with the SilCR signaling peptide and SilD/E export/processing proteins. The presence of an associated bacteriocin region suggests this system may play a role in competitive interactions with other microbes. Comparative analysis of 42 Streptococcus Anginosus/Milleri Group (SAG) genomes reveals this to be a hot spot for genomic variability. A cluster of bacteriocin/immunity genes is found adjacent to the sil system in most SAG isolates (typically 6–10 per strain). In addition, there were two distinct SilCR peptides identified in this group, denoted here as SilCRSAG-A and SilCRSAG-B, with corresponding alleles in silB. Our analysis of the 42 sil loci showed that SilCRSAG-A is only found in Streptococcus intermedius while all three species can carry SilCRSAG-B. In S. intermedius B196, a putative SilA operator is located upstream of bacteriocin gene clusters, implicating the sil system in regulation of microbe–microbe interactions at mucosal surfaces where the group resides. We demonstrate that S. intermedius B196 responds to its cognate SilCRSAG-A, and, less effectively, to SilCRSAG-B released by other Anginosus group members, to produce putative bacteriocins and inhibit the growth of a sensitive strain of S. constellatus.
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Affiliation(s)
- Michelle L Mendonca
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, HamiltonON, Canada
| | - Jake C Szamosi
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton ON, Canada
| | - Anne-Marie Lacroix
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, HamiltonON, Canada
| | - Michelle E Fontes
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, HamiltonON, Canada
| | - Dawn M Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, HamiltonON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, HamiltonON, Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, HamiltonON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, HamiltonON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, HamiltonON, Canada; Department of Medicine, McMaster University, HamiltonON, Canada
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Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DME, Kellner JD, Surette MG. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J 2015; 9:1268. [PMID: 25897775 DOI: 10.1038/ismej.2015.49] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DME, Kellner JD, Surette MG. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J 2015; 9:1246-59. [PMID: 25575312 DOI: 10.1038/ismej.2014.250] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 01/24/2023]
Abstract
The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1-4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.
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Affiliation(s)
| | - Carla J Davidson
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Suzanne McKeon
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Fiona J Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Michelle E Fontes
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dawn M E Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - James D Kellner
- 1] Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada [2] Department of Paediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- 1] Department of Medicine, McMaster University, Hamilton, Ontario, Canada [2] Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada [3] Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Abstract
In response to sudden environmental stress, B. subtilis cells can defer sporulation for multiple cell cycles using a pulsed positive feedback loop. Environmental signals induce diverse cellular differentiation programs. In certain systems, cells defer differentiation for extended time periods after the signal appears, proliferating through multiple rounds of cell division before committing to a new fate. How can cells set a deferral time much longer than the cell cycle? Here we study Bacillus subtilis cells that respond to sudden nutrient limitation with multiple rounds of growth and division before differentiating into spores. A well-characterized genetic circuit controls the concentration and phosphorylation of the master regulator Spo0A, which rises to a critical concentration to initiate sporulation. However, it remains unclear how this circuit enables cells to defer sporulation for multiple cell cycles. Using quantitative time-lapse fluorescence microscopy of Spo0A dynamics in individual cells, we observed pulses of Spo0A phosphorylation at a characteristic cell cycle phase. Pulse amplitudes grew systematically and cell-autonomously over multiple cell cycles leading up to sporulation. This pulse growth required a key positive feedback loop involving the sporulation kinases, without which the deferral of sporulation became ultrasensitive to kinase expression. Thus, deferral is controlled by a pulsed positive feedback loop in which kinase expression is activated by pulses of Spo0A phosphorylation. This pulsed positive feedback architecture provides a more robust mechanism for setting deferral times than constitutive kinase expression. Finally, using mathematical modeling, we show how pulsing and time delays together enable “polyphasic” positive feedback, in which different parts of a feedback loop are active at different times. Polyphasic feedback can enable more accurate tuning of long deferral times. Together, these results suggest that Bacillus subtilis uses a pulsed positive feedback loop to implement a “timer” that operates over timescales much longer than a cell cycle. How long should a cell wait to respond to an environmental change? While many pathways such as those affecting chemotaxis respond to environmental signals quickly, in other contexts a cell may want to defer its response until long after the signal's onset—sometimes waiting multiple cell cycles. How can cells create “timers” to regulate these long deferrals? We study this question in the bacterium Bacillus subtilis, which responds to stress by transforming into a dormant spore. We show that B. subtilis can defer sporulation for extended time periods by first undergoing multiple rounds of growth and proliferation, and only then sporulating. The timer for this deferral is a pulsed positive feedback loop, which ratchets up the concentration of the sporulation master-regulator Spo0A to a critical level over multiple cell cycles. Finally, using mathematical modeling, we illustrate how a novel dynamic feedback mechanism, “polyphasic positive feedback,” lets cells defer sporulation more robustly than with other circuit strategies. Developing techniques that can access pulsing and time-delay dynamics with higher time resolution will enable us to determine if this polyphasic strategy provides a general design principle for the regulation of multi-cell-cycle deferral times seen in other systems.
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Affiliation(s)
- Joe H. Levine
- Howard Hughes Medical Institute and Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
| | - Michelle E. Fontes
- Howard Hughes Medical Institute and Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
| | - Jonathan Dworkin
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Michael B. Elowitz
- Howard Hughes Medical Institute and Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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10
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Eldar A, Chary VK, Xenopoulos P, Fontes ME, Losón OC, Dworkin J, Piggot PJ, Elowitz MB. Partial penetrance facilitates developmental evolution in bacteria. Nature 2009; 460:510-4. [PMID: 19578359 PMCID: PMC2716064 DOI: 10.1038/nature08150] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Accepted: 05/15/2009] [Indexed: 11/09/2022]
Abstract
Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fates of individual organisms differently. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve. Here we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an intercompartmental signalling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable 'twin' spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we can systematically tune the penetrance of each mutant fate. Furthermore, signalling and replication perturbations synergize to significantly increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum shows a strong resemblance to twin sporulation in these B. subtilis mutants. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.
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Affiliation(s)
- Avigdor Eldar
- Howard Hughes Medical Institute and Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA
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