FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3039394038> ?p ?o ?g. }

• W3039394038 endingPage "401.e5" @default.
• W3039394038 startingPage "390" @default.
• W3039394038 abstract "•Bacteriophage/bacteria coexistence is reproduced in murine gut with synthetic microbiota•Bacteriophage resistant clones are not detected over time throughout the gut•Coexistence is not linked to off-target bacteriophage amplification•Spatial distribution and source-sink dynamics support phage-bacteria coexistence The ecological dynamics underlying the coexistence between antagonistic populations of bacteria and their viruses, bacteriophages (phages), in the mammalian gut microbiota remain poorly understood. We challenged a murine synthetic bacterial community with phages to study the factors allowing phages-bacteria coexistence. Coexistence was not dependent on the development of phage-resistant clones nor on the ability of phages to extend their host range. Instead, our data suggest that phage-inaccessible sites in the mucosa serve as a spatial refuge for bacteria. From there, bacteria disseminate in the gut lumen where they are predated by luminal phages fostering the presence of intestinal phage populations. The heterogeneous biogeography of microbes contributes to the long-term coexistence of phages with phage-susceptible bacteria. This observation could explain the persistence of intestinal phages in humans as well as the low efficiency of oral phage therapy against enteric pathogens in animal models and clinical trials. The ecological dynamics underlying the coexistence between antagonistic populations of bacteria and their viruses, bacteriophages (phages), in the mammalian gut microbiota remain poorly understood. We challenged a murine synthetic bacterial community with phages to study the factors allowing phages-bacteria coexistence. Coexistence was not dependent on the development of phage-resistant clones nor on the ability of phages to extend their host range. Instead, our data suggest that phage-inaccessible sites in the mucosa serve as a spatial refuge for bacteria. From there, bacteria disseminate in the gut lumen where they are predated by luminal phages fostering the presence of intestinal phage populations. The heterogeneous biogeography of microbes contributes to the long-term coexistence of phages with phage-susceptible bacteria. This observation could explain the persistence of intestinal phages in humans as well as the low efficiency of oral phage therapy against enteric pathogens in animal models and clinical trials. The mammalian gut is a highly complex and structured organ lined by a variety of eukaryotic cell types that serve the establishment of a mutualistic relationship between the host and different enteric microbes, including viruses. Bacteriophages (phages) are the most abundant viruses residing in the gut, but their precise role in shaping the microbiome remains unclear (Manrique et al., 2017Manrique P. Dills M. Young M.J. The human gut phage community and its implications for health and disease.Viruses. 2017; 9: 141Crossref PubMed Scopus (94) Google Scholar). Changes in the viral and bacterial communities of the gut are increasingly reported to be associated with pathological conditions in humans, including diabetes, inflammatory bowel diseases, and colorectal cancer (Hannigan et al., 2018bHannigan G.D. Duhaime M.B. Ruffin M.T.t. Koumpouras C.C. Schloss P.D. Diagnostic potential and interactive dynamics of the colorectal cancer virome.mBio. 2018; 9 (e02248-18)Crossref PubMed Scopus (52) Google Scholar; Manrique et al., 2017Manrique P. Dills M. Young M.J. The human gut phage community and its implications for health and disease.Viruses. 2017; 9: 141Crossref PubMed Scopus (94) Google Scholar; Zhao et al., 2017Zhao G. Vatanen T. Droit L. Park A. Kostic A.D. Poon T.W. Vlamakis H. Siljander H. Härkönen T. Hämäläinen A.-M. et al.Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.Proc. Natl. Acad. Sci. USA. 2017; 114: E6166-E6175Crossref PubMed Scopus (116) Google Scholar). Although fluctuations in the viral communities have been reported in a recent longitudinal study in humans, a large proportion of individual-specific viral contigs remain detectable over time (months to years), suggesting that individuals possess their own viral fingerprint (Manrique et al., 2016Manrique P. Bolduc B. Walk S.T. van der Oost J. de Vos W.M. Young M.J. Healthy human gut phageome.Proc. Natl. Acad. Sci. USA. 2016; 113: 10400-10405Crossref PubMed Scopus (229) Google Scholar; Shkoporov et al., 2019Shkoporov A.N. Clooney A.G. Sutton T.D.S. Ryan F.J. Daly K.M. Nolan J.A. McDonnell S.A. Khokhlova E.V. Draper L.A. Forde A. et al.The human gut virome is highly diverse, stable, and individual specific.Cell Host Microbe. 2019; 26: 527-541.e5Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar). However, it remains understudied how phages and their corresponding bacterial targets persist together in the gut. Using phage-bacterial model systems, dynamics of the coexistence of predators and preys have been the subject of theoretical and experimental studies, mostly performed in vitro and in silico (Betts et al., 2014Betts A. Kaltz O. Hochberg M.E. Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages.Proc. Natl. Acad. Sci. USA. 2014; 111: 11109-11114Crossref PubMed Scopus (58) Google Scholar; Brockhurst et al., 2006Brockhurst M.A. Buckling A. Rainey P.B. Spatial heterogeneity and the stability of host-parasite coexistence.J. Evol. Biol. 2006; 19: 374-379Crossref PubMed Scopus (58) Google Scholar; Hannigan et al., 2018aHannigan G.D. Duhaime M.B. Koutra D. Schloss P.D. Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.PLoS Comput. Biol. 2018; 14: e1006099Crossref PubMed Scopus (18) Google Scholar; Lenski and Levin, 1985Lenski R.E. Levin B.R. Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communities.The American Naturalist. 1985; 125: 585-602Crossref Scopus (286) Google Scholar; Weitz et al., 2013Weitz J.S. Poisot T. Meyer J.R. Flores C.O. Valverde S. Sullivan M.B. Hochberg M.E. Phage-bacteria infection networks.Trends Microbiol. 2013; 21: 82-91Abstract Full Text Full Text PDF PubMed Scopus (169) Google Scholar). In the mammalian gut, the interaction of phages and bacteria has been explored in mice and pigs (Galtier et al., 2016Galtier M. De Sordi L. Maura D. Arachchi H. Volant S. Dillies M.A. Debarbieux L. Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition.Environ. Microbiol. 2016; 18: 2237-2245Crossref PubMed Scopus (64) Google Scholar; Looft et al., 2014Looft T. Allen H.K. Cantarel B.L. Levine U.Y. Bayles D.O. Alt D.P. Henrissat B. Stanton T.B. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.ISME J. 2014; 8: 1566-1576Crossref PubMed Scopus (205) Google Scholar; Maura et al., 2012aMaura D. Galtier M. Le Bouguénec C. Debarbieux L. Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine.Antimicrob. Agents Chemother. 2012; 56: 6235-6242Crossref PubMed Scopus (55) Google Scholar, Maura et al., 2012bMaura D. Morello E. du Merle L. Bomme P. Le Bouguénec C. Debarbieux L. Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice.Environ. Microbiol. 2012; 14: 1844-1854Crossref PubMed Scopus (47) Google Scholar; Reyes et al., 2013Reyes A. Wu M. McNulty N.P. Rohwer F.L. Gordon J.I. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.Proc. Natl. Acad. Sci. USA. 2013; 110: 20236-20241Crossref PubMed Scopus (177) Google Scholar; Weiss et al., 2009Weiss M. Denou E. Bruttin A. Serra-Moreno R. Dillmann M.L. Brüssow H. In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli.Virology. 2009; 393: 16-23Crossref PubMed Scopus (61) Google Scholar; Yen et al., 2017Yen M. Cairns L.S. Camilli A. A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models.Nat. Commun. 2017; 8: 14187Crossref PubMed Scopus (94) Google Scholar), while human data are derived from metagenomics studies (Manrique et al., 2017Manrique P. Dills M. Young M.J. The human gut phage community and its implications for health and disease.Viruses. 2017; 9: 141Crossref PubMed Scopus (94) Google Scholar; Shkoporov et al., 2019Shkoporov A.N. Clooney A.G. Sutton T.D.S. Ryan F.J. Daly K.M. Nolan J.A. McDonnell S.A. Khokhlova E.V. Draper L.A. Forde A. et al.The human gut virome is highly diverse, stable, and individual specific.Cell Host Microbe. 2019; 26: 527-541.e5Abstract Full Text Full Text PDF PubMed Scopus (121) Google Scholar) and few clinical trials of phage therapy (Sarker and Brüssow, 2016Sarker S.A. Brüssow H. From bench to bed and back again: phage therapy of childhood Escherichia coli diarrhea.Ann. N. Y. Acad. Sci. 2016; 1372: 42-52Crossref PubMed Scopus (29) Google Scholar). Studies in mice have shown that virulent phages have a limited effect on the targeted bacterial populations within the gut (Bhandare et al., 2019Bhandare S. Colom J. Baig A. Ritchie J.M. Bukhari H. Shah M.A. Sarkar B.L. Su J. Wren B. Barrow P. Atterbury R.J. Reviving phage therapy for the treatment of cholera.J. Infect. Dis. 2019; 219: 786-794Crossref PubMed Scopus (13) Google Scholar; Galtier et al., 2017Galtier M. De Sordi L. Sivignon A. de Vallée A. Maura D. Neut C. Rahmouni O. Wannerberger K. Darfeuille-Michaud A. Desreumaux P. et al.Bacteriophages targeting adherent invasive Escherichia coli strains as a promising new treatment for Crohn's disease.J. Crohns Colitis. 2017; 11: 840-847PubMed Google Scholar; Maura et al., 2012aMaura D. Galtier M. Le Bouguénec C. Debarbieux L. Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine.Antimicrob. Agents Chemother. 2012; 56: 6235-6242Crossref PubMed Scopus (55) Google Scholar; Weiss et al., 2009Weiss M. Denou E. Bruttin A. Serra-Moreno R. Dillmann M.L. Brüssow H. In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli.Virology. 2009; 393: 16-23Crossref PubMed Scopus (61) Google Scholar). Nevertheless, both phage and bacterial populations could persist in the gut of animals for several weeks (Maura and Debarbieux, 2012Maura D. Debarbieux L. On the interactions between virulent bacteriophages and bacteria in the gut.Bacteriophage. 2012; 2: 229-233Crossref PubMed Google Scholar; Maura et al., 2012bMaura D. Morello E. du Merle L. Bomme P. Le Bouguénec C. Debarbieux L. Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice.Environ. Microbiol. 2012; 14: 1844-1854Crossref PubMed Scopus (47) Google Scholar). Likewise, a large randomized phage therapy trial targeting Escherichia coli diarrhea in Bangladeshi children showed no evidence for in vivo amplification of oral phages in the gut despite their persistence (Sarker et al., 2016Sarker S.A. Sultana S. Reuteler G. Moine D. Descombes P. Charton F. Bourdin G. McCallin S. Ngom-Bru C. Neville T. et al.Oral phage therapy of acute bacterial diarrhea With two coliphage preparations: A randomized trial in children From Bangladesh.EBioMedicine. 2016; 4: 124-137Abstract Full Text Full Text PDF PubMed Scopus (196) Google Scholar). A similar situation was described in the human gut where the crAssphage coexists with its highly abundant Bacteriodetes bacterial host (Guerin et al., 2018Guerin E. Shkoporov A. Stockdale S.R. Clooney A.G. Ryan F.J. Sutton T.D.S. Draper L.A. Gonzalez-Tortuero E. Ross R.P. Hill C. Biology and Taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut.Cell Host Microbe. 2018; 24: 653-664.e6Abstract Full Text Full Text PDF PubMed Scopus (73) Google Scholar; Shkoporov et al., 2018Shkoporov A.N. Khokhlova E.V. Fitzgerald C.B. Stockdale S.R. Draper L.A. Ross R.P. Hill C. ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis.Nat. Commun. 2018; 9: 4781Crossref PubMed Scopus (109) Google Scholar; Yutin et al., 2018Yutin N. Makarova K.S. Gussow A.B. Krupovic M. Segall A. Edwards R.A. Koonin E.V. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.Nat. Microbiol. 2018; 3: 38-46Crossref PubMed Scopus (110) Google Scholar). Three recent studies showed that administration of virulent phages can also strongly impact the intestinal colonization of their targeted bacteria and nevertheless, still support long-term coexistence (Duan et al., 2019Duan Y. Llorente C. Lang S. Brandl K. Chu H. Jiang L. White R.C. Clarke T.H. Nguyen K. Torralba M. et al.Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease.Nature. 2019; 575: 505-511Crossref PubMed Scopus (151) Google Scholar; Gogokhia et al., 2019Gogokhia L. Buhrke K. Bell R. Hoffman B. Brown D.G. Hanke-Gogokhia C. Ajami N.J. Wong M.C. Ghazaryan A. Valentine J.F. et al.Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis.Cell Host Microbe. 2019; 25: 285-299.e8Abstract Full Text Full Text PDF PubMed Scopus (124) Google Scholar; Hsu et al., 2019Hsu B.B. Gibson T.E. Yeliseyev V. Liu Q. Lyon L. Bry L. Silver P.A. Gerber G.K. Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model.Cell Host Microbe. 2019; 25: 803-814.e5Abstract Full Text Full Text PDF PubMed Scopus (112) Google Scholar). The experimental settings of these studies could account for differences in the amplitude of the impact, notably because of the use of axenic mice, characterized by an immature immune system, and thus, unstable colonization of bacteria of human origin. Moreover, the limited number of phages and bacteria couples that have been studied in the gut environment does not allow yet drawing conclusions on the type and prominence of factors that influence phage-bacterium interactions. Since phages are proposed as a treatment for the major public health threat of antibiotic-resistant bacterial infections (Roach and Debarbieux, 2017Roach D.R. Debarbieux L. Phage therapy: awakening a sleeping giant.Emerging Top. Life Sci. 2017; 1: 93-103Crossref Scopus (47) Google Scholar) as well as means to precisely engineer the intestinal microbiota, further insight into the variety of phage-bacterium interactions and their coexistence in the mammalian gut are deeply needed (Brüssow, 2017Brüssow H. Phage therapy for the treatment of human intestinal bacterial infections: soon to be a reality?.Expert Rev. Gastroenterol. Hepatol. 2017; 11: 785-788Crossref PubMed Scopus (17) Google Scholar). Several factors were shown or proposed to be involved in this coexistence, such as (1) arms race dynamics with resistance development to phage infection and viral counter-resistance, (2) the inherent or evolved ability of the phage to infect multiple hosts, and (3) the distribution of these two antagonistic populations into distinct spatial structures (Brockhurst et al., 2006Brockhurst M.A. Buckling A. Rainey P.B. Spatial heterogeneity and the stability of host-parasite coexistence.J. Evol. Biol. 2006; 19: 374-379Crossref PubMed Scopus (58) Google Scholar; De Sorti et al., 2017De Sorti L. Khanna V. Debarbieux L. The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses.Cell Host Microbe. 2017; 22: 801-808Abstract Full Text Full Text PDF PubMed Scopus (57) Google Scholar; Doron et al., 2018Doron S. Melamed S. Ofir G. Leavitt A. Lopatina A. Keren M. Amitai G. Sorek R. Systematic discovery of antiphage defense systems in the microbial pangenome.Science. 2018; 359: eaar4120Crossref PubMed Scopus (234) Google Scholar; Heilmann et al., 2012Heilmann S. Sneppen K. Krishna S. Coexistence of phage and bacteria on the boundary of self-organized refuges.Proc. Natl. Acad. Sci. USA. 2012; 109: 12828-12833Crossref PubMed Scopus (64) Google Scholar; Hilborn, 1975Hilborn R. The effect of spatial heterogeneity on the persistence of predator-prey interactions.Theor. Popul. Biol. 1975; 8: 346-355Crossref PubMed Scopus (68) Google Scholar; Labrie et al., 2010Labrie S.J. Samson J.E. Moineau S. Bacteriophage resistance mechanisms.Nat. Rev. Microbiol. 2010; 8: 317-327Crossref PubMed Scopus (1185) Google Scholar). In this report, we investigated the contribution of these factors using the synthetic oligo-mouse-microbiota comprising 12 distinct strains (OMM12) (Brugiroux et al., 2016Brugiroux S. Beutler M. Pfann C. Garzetti D. Ruscheweyh H.J. Ring D. Diehl M. Herp S. Lötscher Y. Hussain S. et al.Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.Nat. Microbiol. 2016; 2: 16215Crossref PubMed Scopus (136) Google Scholar). This animal model allows following defined pairs of phages and bacteria in the gut without the need of antibiotic treatments as a confounding factor commonly used to study enteric pathogens in murine models (Croswell et al., 2009Croswell A. Amir E. Teggatz P. Barman M. Salzman N.H. Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection.Infect. Immun. 2009; 77: 2741-2753Crossref PubMed Scopus (191) Google Scholar). In addition, it provides more realistic conditions than mono-colonized mice that lack aspects of competitive and synergistic interspecies interactions of microbes (Weiss et al., 2009Weiss M. Denou E. Bruttin A. Serra-Moreno R. Dillmann M.L. Brüssow H. In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli.Virology. 2009; 393: 16-23Crossref PubMed Scopus (61) Google Scholar). We established stable colonization of two E. coli strains in gnotobiotic OMM12 mice and studied the population dynamics of these strains in the presence of virulent phages. We found that phages were less abundant in the mucosal part of the gut compared with E. coli levels. Our data are in agreement with the ecological theory of source-sink dynamics (Holt, 1985Holt R.D. Population-dynamics in two-patch environments: some anomalous consequences of an optimal habitat distribution.Theor. Popul. Biol. 1985; 28: 181-208Crossref Scopus (531) Google Scholar), providing an explanation for the lack for phage-resistant mutant selection and the limited efficacy of virulent phages in reducing intestinal bacterial loads. Mice harboring the OMM12 consortium (Acutalibacter muris, Akkermansia muciniphila, Bacteroides caecimuris, Bifidobacterium longum subsp animalis, Blautia coccoides, Clostridium clostridioforme, Clostridium innocuum, Enterococcus faecalis, Flavonifractor plautii, Lactobacillus reuteri, Muribaculum intestinale, and Turicimonas muris) were exposed to the murine E. coli commensal strain Mt1B1 to test its capacity to establish in this synthetic community. Mice became colonized with this strain within 2 to 3 days. The fecal levels of strain Mt1B1 remained stable over a period of 2 weeks (Figure 1A). Mice did not exhibit signs of discomfort or change in feces consistency. Twelve days after inoculation of strain Mt1B1, intestinal sections (ileum and colon) were examined, and the location of strain Mt1B1 was determined by fluorescence in situ hybridization (FISH) (Figures 1B and S1). Strain Mt1B1 was found in all sections of the gut, including the ileum, consistent with the location from which it was isolated (mucosa from the ileum of conventional laboratory mice) (Garzetti et al., 2018Garzetti D. Eberl C. Stecher B. Complete genome sequencing of the mouse intestinal isolate Escherichia coli Mt1B1.Genome Announc. 2018; 6 (e00426–18)Crossref PubMed Scopus (1) Google Scholar; Lagkouvardos et al., 2016Lagkouvardos I. Pukall R. Abt B. Foesel B.U. Meier-Kolthoff J.P. Kumar N. Bresciani A. Martínez I. Just S. Ziegler C. et al.The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.Nat. Microbiol. 2016; 1: 16131Crossref PubMed Scopus (173) Google Scholar). We isolated several phages infecting strain Mt1B1 from the environment and selected three (Mt1B1_P3, Mt1B1_P10, and Mt1B1_P17) with different characteristics (host range, adsorption and lysis kinetics, and genomic content) (Figure S2; Tables 1, S1, S2, and S3). Both, Podoviridae P3 and P10 are close to E. coli phages K1F and K1E, respectively, which are capsule-specific phages. Myoviridae P17 is closely related to E. coli phages phAPEC8 and ESCO13. Like ESCO13 and by contrast to phAPEC8, Mt1B1_P17 does not carry an endo-N-acetylneuraminidase gene involved in the degradation of the K1 capsule and, therefore, is most likely not capsule specific (Trotereau et al., 2017Trotereau A. Gonnet M. Viardot A. Lalmanach A.C. Guabiraba R. Chanteloup N.K. Schouler C. Complete genome sequences of two Escherichia coli phages, vB_EcoM_ ESCO5 and vB_EcoM_ESCO13, which are related to phAPEC8.Genome Announc. 2017; 5 (e01337-16)Crossref PubMed Scopus (5) Google Scholar). In liquid broth phages P3 and P10 displayed similar infection kinetics patterns on strain Mt1B1, with rapid lysis followed by a moderate bacterial regrowth at 1.5 h. In contrast, phage P17 halted the growth of strain Mt1B1 for several hours and slow bacterial regrowth resumed only after more than 10 h (Figure 2A). When used in combination, these three phages caused rapid lysis of strain Mt1B1 followed by very slow regrowth (Figure 2A). Then, we assessed the capacity of each phage to replicate in gut sections collected from Mt1B1-colonized OMM12 mice in an ex vivo assay previously used to reveal the activities of phages along different gut sections (Galtier et al., 2017Galtier M. De Sordi L. Sivignon A. de Vallée A. Maura D. Neut C. Rahmouni O. Wannerberger K. Darfeuille-Michaud A. Desreumaux P. et al.Bacteriophages targeting adherent invasive Escherichia coli strains as a promising new treatment for Crohn's disease.J. Crohns Colitis. 2017; 11: 840-847PubMed Google Scholar; Maura et al., 2012aMaura D. Galtier M. Le Bouguénec C. Debarbieux L. Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine.Antimicrob. Agents Chemother. 2012; 56: 6235-6242Crossref PubMed Scopus (55) Google Scholar). We collected samples of the ileum and colon from Mt1B1-colonized OMM12 mice. We then separated out the mucosal and luminal parts of the ileum and colonic tissues. We compared the replication of the three phages in these samples ex vivo with their replication on Mt1B1 planktonic cultures, at both exponential and stationary growth phases. All three phages displayed similar patterns with efficient replication in all tested gut sections and in exponential growth phase liquid culture, whereas no amplification was observed in cells at stationary phase (Figure 2B). As strain Mt1B1 did not multiply in the stationary growth phase (gray bars in Figure 2B), we concluded that Mt1B1 cell growth is necessary for amplification of these three phages.Table 1Main Characteristics of Mt1B1 Phages P3, P10, and P17Mt1B1_P3Mt1B1_P10Mt1B1_P17FamilyPodoviridaePodoviridaeMyoviridaeSubfamilyAutographivirinaeAutographivirinaeunclassifiedGenusTeseptimavirusZindervirusunclassifiedGenome size (kb)40.345.4151.2Number of predicted ORFs4754284Genes unknown function (%)40.464.394.7Affinity constant (mL.min−1)5.26 × 10−10± 2.8 × 10−104.60 × 10−10± 2.15 × 10−101.83 × 10−10± 5.60 × 10−11Adsorption of 90% of phage (min)2.8 ± 0.142.03 ± 0.195.53 ± 1.28 Open table in a new tab Next, we evaluated the transit time of Mt1B1 phages at 6, 24, 48, and 72 h in axenic mice that received a single oral dose (6 × 107 plaque-forming unit [PFU]) of a mixture of the three phages (equal amounts of each phage). The fecal level of Mt1B1 phages was below the threshold at 6 h, maximum at 24 h and then decreased at 48 h and finally reached the limit of detection at 72 h (Figure 3A). In gut sections, we found that the level of phages at 6 h reached 106, 104, and 103 PFU/g in the luminal part of the ileum, the mucosal part of the ileum, and the luminal part of the colon, respectively, whereas it remained undetected in the mucosal part of the colon. At 24 h the level of phages in the ileum dropped, whereas it increased in the colon, and at 48 h it was barely detectable in the ileum while only present in the luminal part of the colon. At 72 h the level of phages was below the threshold of detection in all gut sections tested (Figure 3B). Then, we performed a similar experiment in OMM12 mice, not inoculated with strain Mt1B1, by taking samples at 24 and 48 h post-gavage (same dose as above). Phage levels in feces were slightly lower than those observed in axenic mice. We could detect phages only in the luminal part of the colon at both 24 and 48 h post-gavage as anticipated from experiments with axenic mice (Figure 3C). These findings indicate that none of the Mt1B1 phages amplified in vivo on any of the 12 strains ruling out a possible off-target amplification. These data are in agreement with previous results on phage safety from human volunteers and from conventional mice not colonized with the targeted bacteria (Bruttin and Brüssow, 2005Bruttin A. Brüssow H. Human volunteers receiving Escherichia coli phage T4 orally: a safety test of phage therapy.Antimicrob. Agents Chemother. 2005; 49: 2874-2878Crossref PubMed Scopus (365) Google Scholar; Maura et al., 2012bMaura D. Morello E. du Merle L. Bomme P. Le Bouguénec C. Debarbieux L. Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice.Environ. Microbiol. 2012; 14: 1844-1854Crossref PubMed Scopus (47) Google Scholar; Weiss et al., 2009Weiss M. Denou E. Bruttin A. Serra-Moreno R. Dillmann M.L. Brüssow H. In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli.Virology. 2009; 393: 16-23Crossref PubMed Scopus (61) Google Scholar). We next investigated how Mt1B1-colonized OMM12 mice responded to an identical single oral dose of the three phages (6 × 107 PFU). The fecal levels of phages and bacteria were monitored at short (4 and 6 h post-oral dose) and long (during 2 weeks) periods of time (Figure S3A). At all time points but one (day 18 [d18]) following phage administration, levels of Mt1B1 in the phage group were lower than in the control group, despite remaining within one-log of variation and not reaching significance. Within the two weeks of observation phage levels fluctuated within 2 logs (Figure S3B). Nevertheless, phage:bacteria ratios remained stable (less than 1 log variation) over time (Figure S3C). These data show that a single dose of these three phages is sufficient to initiate their long-term replication in Mt1B1-colonized OMM12 mice indicating that this animal model is suitable to study the coexistence of phages and bacteria in the gut. Afterward, we asked whether repeating the phages administration during three consecutive days could disturb this coexistence between phages and strain Mt1B1. Such a setting mimics a phage therapy treatment targeting bacterial pathogens residing in the human gut (Corbellino et al., 2020Corbellino M. Kieffer N. Kutateladze M. Balarjishvili N. Leshkasheli L. Askilashvili L. Tsertsvadze G. Rimoldi S.G. Nizharadze D. Hoyle N. et al.Eradication of a multi-drug resistant, carbapenemase-producing Klebsiella pneumoniae isolate following oral and intra-rectal therapy with a custom-made, lytic bacteriophage preparation.Clin. Infect. Dis. 2020; 70: 1998-2001Crossref PubMed Scopus (24) Google Scholar). In two independent experiments, we observed a small but significant decrease in the fecal levels of strain Mt1B1 when comparing phage-treated and control groups (d15, p = 0.0001; d16, p = 0.002; d17, p = 0.023) (Figure 4A; Table S4). Despite this significant impact, phage levels and phage:bacteria ratios remained stable (within 1-log) (Figures 4B and 4C) and were comparable to data obtained with a single dose of phages showing that the three consecutive phage administrations did not destabilize phage-bacteria coexistence (Figure S3). We next assessed the stability of the gut microbiota of both phage-treated (n = 6) and non-treated (n = 5) mice groups by two methods, 16S rRNA specific qPCR (Brugiroux et al., 2016Brugiroux S. Beutler M. Pfann C. Garzetti D. Ruscheweyh H.J. Ring D. Diehl M. Herp S. Lötscher Y. Hussain S. et al.Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.Nat. Microbiol. 2016; 2: 16215Crossref PubMed Scopus (136) Google Scholar) and 16S amplicon sequencing. This quantification was performed at d0 (before colonization with strain Mt1B1), d14 (before the gavage with the three phages), and d17 (1 day after the third phages gavage), and both methods showed similar results (Figure S4). Changes in the bacterial community (qPCR data) were analyzed by performing a between-class principal component analysis (PCA), taking into account days, cages, and phage inoculation. Results identified daily fluctuations as the main source of the observed variations regardless of the presence or absence of phages (Figure 4D; Table S5). This finding is also consistent with the passive transit of these phages in OMM12 devoid of E. coli strain Mt1B1 (Figure 3C). Therefore, the replication of phages observed in Mt1B1-colonized OMM12 mice result exclusively from their capacity to infect strain Mt1B1 in the gut environment, confirming the lack of a possible off-target amplification to support phage coexistence. Next, we tested whether the emergence of phage-resistant clones could explain how bacteria can coexist with phages. A total of 280 isolated fecal clones of strain Mt1B1" @default.
• W3039394038 created "2020-07-10" @default.
• W3039394038 creator A5005187562 @default.
• W3039394038 creator A5007212973 @default.
• W3039394038 creator A5025183386 @default.
• W3039394038 creator A5028175486 @default.
• W3039394038 creator A5029530582 @default.
• W3039394038 creator A5060888680 @default.
• W3039394038 creator A5068346044 @default.
• W3039394038 creator A5076189110 @default.
• W3039394038 creator A5078012380 @default.
• W3039394038 creator A5079237100 @default.
• W3039394038 date "2020-09-01" @default.
• W3039394038 modified "2023-10-18" @default.
• W3039394038 title "The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages" @default.
• W3039394038 cites W122717592 @default.
• W3039394038 cites W1534466504 @default.
• W3039394038 cites W1799098265 @default.
• W3039394038 cites W1974477809 @default.
• W3039394038 cites W1981069592 @default.
• W3039394038 cites W1987487254 @default.
• W3039394038 cites W1990575687 @default.
• W3039394038 cites W1990947402 @default.
• W3039394038 cites W2004548026 @default.
• W3039394038 cites W2005210068 @default.
• W3039394038 cites W2008733625 @default.
• W3039394038 cites W2011223551 @default.
• W3039394038 cites W2019197162 @default.
• W3039394038 cites W2026473901 @default.
• W3039394038 cites W2029070458 @default.
• W3039394038 cites W2034090239 @default.
• W3039394038 cites W2036580479 @default.
• W3039394038 cites W2044111860 @default.
• W3039394038 cites W2045119482 @default.
• W3039394038 cites W2057460314 @default.
• W3039394038 cites W2079032703 @default.
• W3039394038 cites W2087445504 @default.
• W3039394038 cites W2095162986 @default.
• W3039394038 cites W2099670135 @default.
• W3039394038 cites W2110886653 @default.
• W3039394038 cites W2126178176 @default.
• W3039394038 cites W2126331514 @default.
• W3039394038 cites W2127634163 @default.
• W3039394038 cites W2131891835 @default.
• W3039394038 cites W2148103005 @default.
• W3039394038 cites W2168670250 @default.
• W3039394038 cites W2224386098 @default.
• W3039394038 cites W2296724767 @default.
• W3039394038 cites W2347061404 @default.
• W3039394038 cites W2396113366 @default.
• W3039394038 cites W2397620631 @default.
• W3039394038 cites W2468409351 @default.
• W3039394038 cites W2469470522 @default.
• W3039394038 cites W2511649068 @default.
• W3039394038 cites W2526966274 @default.
• W3039394038 cites W2547407637 @default.
• W3039394038 cites W2549269050 @default.
• W3039394038 cites W2555392883 @default.
• W3039394038 cites W2563721064 @default.
• W3039394038 cites W2584789564 @default.
• W3039394038 cites W2601239536 @default.
• W3039394038 cites W2606644876 @default.
• W3039394038 cites W2623963207 @default.
• W3039394038 cites W2626160405 @default.
• W3039394038 cites W2735006823 @default.
• W3039394038 cites W2745133479 @default.
• W3039394038 cites W2767759966 @default.
• W3039394038 cites W2768753817 @default.
• W3039394038 cites W2770624394 @default.
• W3039394038 cites W2784532673 @default.
• W3039394038 cites W2800588250 @default.
• W3039394038 cites W2803917190 @default.
• W3039394038 cites W2807807289 @default.
• W3039394038 cites W2885273563 @default.
• W3039394038 cites W2900199636 @default.
• W3039394038 cites W2900323450 @default.
• W3039394038 cites W2912457922 @default.
• W3039394038 cites W2913714888 @default.
• W3039394038 cites W2917868694 @default.
• W3039394038 cites W2918063357 @default.
• W3039394038 cites W2925393305 @default.
• W3039394038 cites W2939969902 @default.
• W3039394038 cites W2947454803 @default.
• W3039394038 cites W2948347995 @default.
• W3039394038 cites W2949665967 @default.
• W3039394038 cites W2949853177 @default.
• W3039394038 cites W2950060642 @default.
• W3039394038 cites W2950868848 @default.
• W3039394038 cites W2953273295 @default.
• W3039394038 cites W2967609754 @default.
• W3039394038 cites W2979358136 @default.
• W3039394038 cites W2988550413 @default.
• W3039394038 cites W4229833877 @default.
• W3039394038 doi "https://doi.org/10.1016/j.chom.2020.06.002" @default.
• W3039394038 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/32615090" @default.
• W3039394038 hasPublicationYear "2020" @default.
• W3039394038 type Work @default.
• W3039394038 sameAs 3039394038 @default.

• next