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The Evolution of Cooperation Within the Gut Microbiota Seth Rakoff-Nahoum1,2, Kevin R

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The Evolution of Cooperation Within the Gut Microbiota Seth Rakoff-Nahoum1,2, Kevin R LETTER doi:10.1038/nature17626 The evolution of cooperation within the gut microbiota Seth Rakoff-Nahoum1,2, Kevin R. Foster3 & Laurie E. Comstock2 Cooperative phenotypes are considered central to the functioning of increased the fitness of the mutants (Fig. 1d, e, Extended Data Fig. 1c, d). microbial communities in many contexts, including communication This is consistent with cooperation via public good availability of via quorum sensing, biofilm formation, antibiotic resistance, and amylopectin and levan breakdown products. pathogenesis1–5. The human intestine houses a dense and diverse 1,2,4–9 microbial community critical to health , yet we know little a SusC homologue Inner membrane monosaccharide importer about cooperation within this important ecosystem. Here we test SusD homologue Fructokinase experimentally for evolved cooperation within the Bacteroidales, GH/SPII Hybrid two component sensor the dominant Gram-negative bacteria of the human intestine. We GH/SPI show that during growth on certain dietary polysaccharides, the Levan model member Bacteroides thetaiotaomicron exhibits only limited cooperation. Although this organism digests these polysaccharides 1763 1762 1761 1760 1759 1758 1757 1754 extracellularly, mutants lacking this ability are outcompeted. In Amylopectin contrast, we discovered a dedicated cross-feeding enzyme system in the prominent gut symbiont Bacteroides ovatus, which digests 3705 3704 3703 3702 3701 3700 3699 3698 polysaccharide at a cost to itself but at a benefit to another species. b Bt WT Bt Δ3698 c Bt WT Bt Δ1760 Using in vitro systems and gnotobiotic mouse colonization models, 0.8 Amylopectin 0.5 Levan we find that extracellular digestion of inulin increases the fitness of ) 0.4 B. ovatus owing to reciprocal benefits when it feeds other gut species 0.6 600 nm A such as Bacteroides vulgatus. This is a rare example of naturally- ( 0.3 evolved cooperation between microbial species. Our study reveals 0.4 0.2 both the complexity and importance of cooperative phenotypes 0.2 within the mammalian intestinal microbiota. 0.1 Absorbance A major challenge facing the study of host-associated microbiotas 0 0 is to understand the ecological and evolutionary dynamics that shape 0204060 0204060 Time (h) these communities2,5,10–13. A key determinant of microbial dynamics is deBt WT S = Start of culture Bt WT the balance of cooperation and competition both within and between Bt Δ3698 E = End at early stationary Bt Δ1760 species2,5,14,15. Here we test for the evolution of cooperation within the 1010 1010 mammalian microbiota by focusing on the Bacteroidales, the most abundant order of Gram-negative bacteria of the human intestine with 109 P = 0.04 109 P = 0.004 9 11 species that co-colonize the host at high densities of 10 –10 CFU per P = 0.0003 P = 0.03 gram of faeces16,17. Members of this order break down polysaccharides 108 108 6,18 outside of their cell using outer surface glycoside hydrolases , some CFU per ml 107 107 of which are secreted on outer membrane vesicles3,19. This suggests a significant potential for one cell to cooperatively feed other cells. 106 106 SE ESEE SEESEE As extracellular digestion is considered important for growth of 1,6,8 Co Co Co Co Bacteroidales on polysaccharides , we focused on this trait as a can- Mono Mono Mono Mono didate for cooperative interactions within the gut microbiota and asked Figure 1 | Direct and cooperative benefits of polysaccharide digestion whether a bacterium that breaks down a polysaccharide extracellularly by surface glycoside hydrolases (GH). a, Polysaccharide utilization loci receives most, or all20, of the benefits of its efforts. of B. thetaiotaomicron (Bt) for amylopectin and levan with the products or We first made isogenic mutants in genes responsible for the extracell- properties each gene encodes listed above and colour-coded. SPI or SPII, ular digestion of polysaccharides in the well-studied human gut strain, signal peptidase I or II cleavage site, respectively. b, c, Growth of Bt wild Bacteroides thetaiotaomicron VPI-5482 (refs 1, 8). Specifically, we deleted type (WT) and surface GH mutants in media with amylopectin (n = 2, the genes encoding the outer surface glycoside hydrolases BT3698 of the cell culture biological replicates) (b) or levan (n = 2, cell culture biological amylopectin/starch utilization locus and BT1760 of the levan utilization replicates) (c). See Extended Data Fig. 1 for additional independent experiments. d, e, Growth of Bt WT and surface GH mutants in mono- locus (Fig. 1a), required for growth on amylopectin and levan, respectively and co-culture in media with amylopectin (n = 2, cell culture biological (Fig. 1b, c, Extended Data Fig. 1a, b). Consistent with previous observa- replicates) (d) or levan (n = 2, cell culture biological replicates) (e). See 1,8 tions , neither mutant grew with the specific polysaccharide in mon- Extended Data Fig. 1 for additional independent experiments. In all panels oculture (Fig. 1b, c, Extended Data Fig. 1a, b). However, co-culture error bars represent standard error; P values derived from two-tailed of ΔBT3698 or ΔBT1760 with wild type in amylopectin or levan Student’s t-test. 1Division of Infectious Diseases, Department of Medicine, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA. 2Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, Massachusetts 02115, USA. 3Department of Zoology and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3PS, UK. 12 MAY 2016 | VOL 533 | NATURE | 255 © 2016 Macmillan Publishers Limited. All rights reserved RESEARCH LETTER a a Bo WT Bo Δ04503 b P = 0.013 Bo Δ04502 Bo Δ04502/3 9 P = 0.019 10 10 NS 04505 04504 04503 04502 04501 04500 04498 04496 2.5 × 10 s b c 108 2.0 × 1010 Bo WT Bo Δ04503 0.5 10 7 1.5 × 10 NS ) Bo Δ04502 Bo Δ04502/3 10 0.4 1.0 × 1010 6 600 nm 10 CFU per patch A 9 CFU per g faece ( 0.3 5.0 × 10 5 10 0 0.2 024 024024 024 PS-free/H 0 PS-free/inulin Day 2 0.1 Absorbance c Inulin d 0 h h h h h h h h h h 0.06% Fru 0.06% Fru + Inulin 2 6 2 6 2 6 020406080 0.06% FOS 0.06% FOS + Inulin 0.5 0.5 0.5 Inulin Digested Inulin Time (h) 0.75 Bo WT 0.5 Bo WT His-04502 His-04503 His-04502 ** + 0.4 pET16b 27 His-04503 0.50 0.3 ** d 0.5% Inulin 0.1% Inulin ) 0.2 0.25 ** 600 nm 0.1 A ( 0 0 020406080 01020304050 0.75 ) 0.5 Bo Δ04502/3 Bo Δ04502 * 600 nm 0.4 Absorbance A 0.50 ( 0.3 *** 0.2 u u St St St St 0.25 St St St St LL LL LL LL LL LL LL LL EL EL EL EL EL EL EL EL ML ML ML ML ML ML ML ML * Fr Fr Inulin Inulin 0.1 Bo Bo Bo Bo Bo Bo Bo Bo Absorbance WT Δ04502 Δ04503 Δ04502/3 WT Δ04502 Δ04503 Δ04502/3 0 0 020406080 01020304050 Time (h) e Bo WT Bo Δ04504 0.5 Bo Δ04502/3 * 0.4 Bo Δ04502/3 Bo Δ04505 Bo WT Bo Δ04502/3 0.4 ) P = 0.03/0.0009 ** 0.3 1.0 0.3 600 nm ) A P < 0.001/= 0.006 ( 0.2 0.8 P = 0.02/0.007 ** 0.2 600 nm A ( 0.6 0.1 0.1 0.4 0 01020304050 Absorbance 0.2 Time (h) 0 020406080 100 Absorbance 0 Time (h) Inulin Inulin Inulin Inulin + + Figure 2 | B. ovatus does not require surface digestion for utilization 0.06% Fru 0.06% Fru of inulin. a, Predicted inulin utilization locus of B. ovatus (Bo). Gene Figure 3 | Cost of inulin digestion by surface glycoside hydrolases. designations shown are preceded by BACOVA_. The colour coding of a, Growth yield of Bo WT and mutants on inulin agarose plates. Each gene products is as in Fig. 1. b, Thin layer chromatography (TLC) analysis line represents n = 1 sample per condition. See Extended Data Fig. 4 of inulin defined medium incubated for the indicated times with purified for additional independent experiments. b, Bacteria per gram of faeces His-tagged 04502, 04503 or 04502 and 04503, or vector control. See of gnotobiotic mice seven days after monocolonization with Bo WT or Supplementary Information Fig. 1 for uncropped scanned images. Δ04502/3 on a polysaccharide-free diet or supplemented with inulin c, Growth of Bo WT and mutants in inulin defined medium. d, TLC (n = 5 biological replicate mice per condition). c, Growth curves (upper analysis of conditioned media during the growth of Bo WT and mutants and middle panels) and maximal A600 nm (bottom panel) of Bo WT or in 0.5% and 0.1% inulin. EL, early log; ML, mid log; LL, late log; Δ04502/3 in minimal media with carbon sources as indicated. Each St, stationary. e, Growth of Bo WT, Δ04502/3, Δ04504 (susD orthologue) line represents n = 1 sample per condition. See Extended Data Fig. 4 for and Δ04505 (susC orthologue) mutants in inulin defined medium. additional independent experiments. In the bottom panel, P values are For c, e, each line represents n = 1 sample per condition. See displayed as paired (matched WT and Δ04502/3 within same experiment) Extended Data Fig. 2 for additional independent experiments. followed by unpaired (all experiments) two-tailed Student’s t-test (n = 7, In all panels error bars represent standard error; P values derived biological replicates).
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