The outer mucus layer hosts a distinct intestinal microbial niche

Li, Hai; Limenitakis, Julien; Fuhrer, Tobias; Geuking, Markus B.; Lawson, Melissa A.; Wyss, Madeleine; Brugiroux, Sandrine; Keller, Irene; Macpherson, Jamie A.; Rupp, Sandra; Stolp, Bettina; Stein, Jens V; Stecher, Bärbel; Sauer, Uwe; McCoy, Kathleen; Macpherson, Andrew J.

doi:10.1038/ncomms9292

Cited by 412 publications

(385 citation statements)

References 69 publications

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“…1, we found that the adherent mucus of germ-free (GF) mice was only ∼25% as thick as that of SPF mice in vivo (Fig. 4B), consistent with previous observations (8,32). Thicker SPF mucus was previously attributed solely to altered mucus secretion by the host in response to the presence of microbes, and not to the difference in polymeric composition of the gut fluid.…”

Section: Applied Physical Sciencessupporting

confidence: 90%

Polymers in the gut compress the colonic mucus hydrogel

Datta

Steinberg

Ismagilov

2016

Proc. Natl. Acad. Sci. U.S.A.

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Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host-microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer-mucus interactions can be described using a thermodynamic model based on Flory-Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice-whose microbiota degrade gut polymers-did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes.hydrogel | biophysics | biomaterials | polymers | mucus B iological hydrogels (including mucus, blood clots, and the extracellular matrix) provide critical functions, yet little is known about how their structure is influenced by materials they come into contact with regularly. For example, the environments of many hydrogels abound in polymers, such as dietary fibers (1, 2) or administered therapeutics (3-5) in the gut and soluble glycoproteins in tissues. Whether such polymers interact with these hydrogels, and if so, how, remains unclear. An important example is the case of colonic mucus, which protects the gut from infection and physical damage (6-8), mediates drug delivery (9), and mediates host-microbe interactions (10) in a structure-dependent manner; for example, a "tighter" mesh could impede the infiltration of microorganisms from the intestinal lumen (6, 11-13). Mucus restructuring is typically attributed solely to changes in secretion (14-16), or to the activity of specific enzymes (8, 17), detergents (18), or dextran sulfate sodium-induced inflammation (19). However, the physicochemical properties of the gut environment itself-particularly its polymeric composition-have not been considered as a potential regulator of mucus structure. We therefore sought to characterize the structure of the colonic mucus hydrogel in the absence and in the presence of polymers. Res...

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Section: Applied Physical Sciencessupporting

confidence: 90%

Polymers in the gut compress the colonic mucus hydrogel

Datta

Steinberg

Ismagilov

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Human gastrointestinal mucus consists of two layers, a thick loosely mucus layer and a thinner layer attached to the mucosa (35). While the inner layer is nearly sterile, the outer mucus layer forms a microbial niche that also includes nonmucolytic bacteria (36,37). One of those bacterial species is E. coli (38).…”

Section: Figmentioning

confidence: 99%

Escherichia coli O157:H7 Strain EDL933 Harbors Multiple Functional Prophage-Associated Genes Necessary for the Utilization of 5- N -Acetyl-9- O -Acetyl Neuraminic Acid as a Growth Substrate

Saile

Voigt

Kessler

et al. 2016

Appl Environ Microbiol

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Enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain EDL933 harbors multiple prophage-associated open reading frames (ORFs) in its genome which are highly homologous to the chromosomal nanS gene. The latter is part of the nanCMS operon, which is present in most E. coli strains and encodes an esterase which is responsible for the monodeacetylation of 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac 2 ). Whereas one prophage-borne ORF (z1466) has been characterized in previous studies, the functions of the other nanS-homologous ORFs are unknown. In the current study, the nanS-homologous ORFs of EDL933 were initially studied in silico. Due to their homology to the chromosomal nanS gene and their location in prophage genomes, we designated them nanS-p and numbered the different nanS-p alleles consecutively from 1 to 10. The two alleles nanS-p2 and nanS-p4 were selected for production of recombinant proteins, their enzymatic activities were investigated, and differences in their temperature optima were found. Furthermore, a function of these enzymes in substrate utilization could be demonstrated using an E. coli C600⌬nanS mutant in a growth medium with Neu5,9Ac 2 as the carbon source and supplementation with the different recombinant NanS-p proteins. Moreover, generation of sequential deletions of all nanS-p alleles in strain EDL933 and subsequent growth experiments demonstrated a gene dose effect on the utilization of Neu5,9Ac 2 . Since Neu5,9Ac 2 is an important component of human and animal gut mucus and since the nutrient availability in the large intestine is limited, we hypothesize that the presence of multiple Neu5,9Ac 2 esterases provides them a nutrient supply under certain conditions in the large intestine, even if particular prophages are lost. IMPORTANCEIn this study, a group of homologous prophage-borne nanS-p alleles and two of the corresponding enzymes of enterohemorrhagic E. coli (EHEC) O157:H7 strain EDL933 that may be important to provide alternative genes for substrate utilization were characterized. Enterohemorrhagic Escherichia coli (EHEC) bacteria are foodborne pathogens that cause severe human gastrointestinal illness characterized by bloody diarrhea and hemolytic-uremic syndrome (HUS) (1, 2). EHEC are very heterogeneous in their genome sizes and structures as well as in their virulence gene composition (3, 4). The major pathogenicity factors of strains of classical EHEC serogroups such as O157, O26, O111, O145, and O103 are production of one or more Shiga toxins (Stx) and development of attaching and effacing lesions in the human large intestine (5). The latter effect is caused by the translocation of effector proteins into eukaryotic cells by a type III secretion system encoded by the locus of enterocyte effacement (LEE) (6). Besides LEE-positive EHEC strains, LEE-negative EHEC strains such as O113:H21 strain 98NK2 and the O104:H4 clone have caused severe human disease and outbreaks (7,8). Stx are generally encoded in the genome of lambdoid phages. EHEC strains can carry one or mor...

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“…Although various plausible hypotheses could explain how the mutations discussed above could be selected in extraintestinal virulence compartments, the human gut itself is a highly dynamic and compartmentalized environment, with oscillating nutrient composition and other physiological conditions (72,73). This could allow adaptive diversification within resident strains via many different mechanisms, including gene inactivation.…”

Section: Discussionmentioning

confidence: 99%

Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli

et al. 2017

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We analyzed the within-household evolution of two household-associated Escherichia coli strains from pandemic clonal group ST131-H30, using isolates recovered from five individuals within two families, each of which had a distinct strain. Family 1's strain was represented by a urine isolate from the index patient (older sister) with recurrent cystitis and a blood isolate from her younger sister with fatal urosepsis. Family 2's strain was represented by a urine isolate from the index patient (father) with pyelonephritis and renal abscesses, blood and kidney drainage isolates from the daughter with emphysematous pyelonephritis, and urine and fecal isolates from the mother with cystitis. Collectively, the several variants of each family's strain had accumulated a total of 8 (family 1) and 39 (family 2) point mutations; no two isolates were identical. Of the 47 total mutations, 36 resulted in amino acid changes or truncation of coded proteins. Fourteen such mutations (39%) targeted genes encoding transcriptional regulators, and 9 (25%) involved DNA-binding transcription factors (TFs), which significantly exceeded the relative contribution of TF genes to the isolates' genomes (ϳ6%). At least one-half of the transcriptional regulator mutations were inactivating, based on phenotypic and/or transcriptional analysis. In particular, inactivating mutations in the global regulator LrhA (repressor of type 1 fimbriae and flagella) occurred in the blood isolates from both households and increased the virulence of E. coli strains in a murine sepsis model. The results indicate that E. coli undergoes adaptive evolution between and/or within hosts, generating subpopulations with distinctive phenotypes and virulence potential.IMPORTANCE The clonal evolution of bacterial strains associated with interhost transmission is poorly understood. We characterized the genome sequences of clonal descendants of two Escherichia coli strains, recovered at different time points from multiple individuals within two households who had different types of urinary tract infection. We found evidence that the E. coli strains underwent extensive mutational diversification between and within these individuals, driven disproportionately by inactivation of transcriptional regulators. In urosepsis isolates, the mutations observed in the global regulator LrhA increased bacterial virulence in a murine sepsis model. Our findings help in understanding the adaptive dynamics and strategies of E. coli during short-term natural evolution.

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The outer mucus layer hosts a distinct intestinal microbial niche

Cited by 412 publications

References 69 publications

Polymers in the gut compress the colonic mucus hydrogel

Polymers in the gut compress the colonic mucus hydrogel

Escherichia coli O157:H7 Strain EDL933 Harbors Multiple Functional Prophage-Associated Genes Necessary for the Utilization of 5- N -Acetyl-9- O -Acetyl Neuraminic Acid as a Growth Substrate

Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli

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