Gut microbiota composition correlates with diet and health …

RESEARCH ARTICLE

Ruminococcus , Oscillibacter , Alistipes and the central Odoribacter CAG. These CAG relationships are termed Wiggum plots, in which genus abundance can be represented as discs proportional to abund- ance (Supplementary Fig. 12), to normalized over-abundance (Fig. 4), or to differential over-abundance (Supplementary Fig. 13). In the Wiggum plot corresponding to the whole cohort (Supplementary Fig. 12), the path away from the Ruminococcus CAG towards the Oscillibacter CAG shows a reduced number of genera that make butyrate, and an increased number able to metabolize fermentation products. To simplify the microbiota data for health correlation, we used the eight subject divisions identified by OTU clustering (Fig. 1c). These eight divisions were superimposed on a UniFrac PCoA analysis of the data in Fig. 1a, defining 8 subject groups (Fig. 4, Groups 1A through 4B). These are separation points within a microbiota composition spectrum that represent groups of individuals who have significantly different microbiota as defined by the permutation multivariate ana- lysis of variance (MANOVA) test on unweighted UniFrac data. We then constructed individual Wiggum plots for the microbiota in these 8 groups (Fig. 4). The transition from healthy community-dwelling subjects, to frail long-term care residents, is accompanied by distinctive CAG dominance, most significantly in abundances of Prevotella and Ruminococcus CAGs (community associated CAGs) and Alistipes and Oscillibacter CAGs (long-stay-associated CAGs). Our analysis of Fig. 4 suggested two paths from community- associated health to long-stay-associated frailty (plot 1A–4A, and 1B–4B), which were examined with reference to health correlations

associated with markers for increased frailty and poorer health, having adjusted for gender, age and location. Because location largely determines diet (Fig. 2), adjusting for location reduces the effect of diet, and as there was also clear evidence for microbiota–health asso- ciations within the long-stay setting, we infer that the causal relation- ship is in a diet–microbiota–health direction. Microbiota structure and healthy ageing Gut microbiota can be assigned to one of three enterotypes 34 ,drivenby Bacteroides , Prevotella and Ruminococcus species. A recent study detected only the Bacteroides and Prevotella enterotypes, which were associated with diets rich in protein and carbohydrate, respectively 21 . Using those methods, we predicted an optimal number of two clusters using five out of six methodologies, albeit with weaker support than previous studies (Supplementary Fig. 11). In line with a previous study 21 , the two clusters associated with Bacteroides and Prevotella , but not with Ruminococcus . Although enterotype assignments from the three approaches were very different (Supplementary Fig. 11), community subjects were more frequently of the Prevotella enterotype. To identify patterns in the microbiota, we established co-abundance associations of genera (Supplementary Fig. 12a), and then clustered correlated genera into six co-abundance groups (CAGs) (Supplemen- tary Fig. 12b). These are not alternatives to enterotypes, which are subject-driven and poorly supported in this elderly cohort, but they describe the microbiota structures found across the subject groups in statistically significant co-abundance groups (Supplementary Notes). The dominant genera in these CAGs were Bacteroides , Prevotella ,

Sporobacter

Acidaminobacter

Rikenella

Sporobacter Acetivibrio

Ethanoligenens

Oscillibacter Acetivibrio Akkermansia Methanobrevibacter Howardella Acetitomaculum

Parabacteroides

Desulfovibrio Robinsoniella

Rikenella

Eubacterium

Anaerophaga

Robinsoniella

Anaerovorax

Alistipes

Methanobrevibacter

Papillibacter

Prevotella

Bulleidia

Acidaminococcus

Lactonifactor Anaerofilum Acetanaerobacterium Coprobacillus Sedimentibacter Cloacibacillus Eggerthella Bifidobacterium

Akkermansia

Natronincola

Cerasicoccus

Clostridium Sporacetigenium Alkaliphilus

Victivallis

Anaerotruncus Lutispora

Tepidibacter

Clostridium

Escherichia/Shigella

Hydrogenoanaerobacterium

Hespellia

Victivallis

Sarcina Lachnobacterium Peptococcus

Butyricimonas

Herbaspirillum

Butyricimonas

Holdemania

Odoribacter

Peptococcus

Weissella

Coprococcus

Anaerosporobacter

Catenibacterium

Parasporobacterium

Parasutterella Barnesiella Oribacterium

Paraprevotella Syntrophococcus

Acidaminobacter

Ethanoligenens Rikenella

Sporobacter

Ethanoligenens

Acetivibrio

Oscillibacter

Parabacteroides

Robinsoniella

Anaerovorax

Mogibacterium Akkermansia Anaerovorax

Papillibacter

Methanobrevibacter Desulfovibrio

Methanobrevibacter

Eubacterium

Cloacibacillus

Anaerophaga

IL-8 IL-6

Mogibacterium

Subdoligranulum Lutispora Anaerotruncus

Anaerofilum

Bulleidia

Prevotella Clostridium Sporacetigenium Victivallis Alkaliphilus Howardella

Acidaminococcus Rothia

Eggerthella

Sedimentibacter

Natronincola

Cerasicoccus

Tepidibacter

Lactonifactor

Coprobacillus

MNA Diastolic BP

Hydrogenoanaerobacterium

Bifidobacterium

Holdemania

Phascolarctobacterium

Leuconostoc

Herbaspirillum

Weissella

IL-8

Lachnobacterium

Phascolarctobacterium

Peptococcus

Coprococcus

Streptophyta

Pseudobutyrivibrio

Butyricicoccus

Veillonella

Catenibacterium Parasporobacterium

Oribacterium Dialister

Diastolic BP CRP Systolic BP

Anaerostipes

Ruminococcus

Weight CC

Barthel FIM

Actinobacillus Sutterella

Paraprevotella

Barnesiella

Anaerostipes

IL-6

2B 3B

red 4B

Sporobacter

Ethanoligenens

Oscillibacter

Akkermansia

Eubacterium

Dorea Anaerofilum

Anaerophaga

Anaerofilum

Acetanaerobacterium

Lactococcus Eggerthella

Prevotella Bulleidia Natronincola Clostridium Sporacetigenium Howardella

Lutispora

Subdoligranulum

Oxobacter

Rothia

Lactonifactor

Barthel FIM MNA CC

Escherichia/Shigella Coprobacillus

Anaerotruncus

Hespellia

Hydrogenoanaerobacterium

Actinomyces

Butyricimonas

GDT

Actinomyces

Lactobacillus

Weissella

Leuconostoc

Odoribacter

Leuconostoc

Lachnobacterium Coprococcus

GDT Diastolic BP

Bacteroides

MMSE Weight BMI Diastolic BP

Streptophyta

Pseudobutyrivibrio Dialister

Sharpea

Butyricicoccus

Ruminococcus Roseburia Veillonella Faecalibacterium Streptococcus Asaccharobacter Blautia Moryella Anaerostipes

Blautia

Catenibacterium Parasporobacterium

Veillonella

Oribacterium

Streptococcus

Actinobacillus

Syntrophococcus

Parasutterella

Rikenella

Oscillibacter

Barnesiella

Parabacteroides

Alistipes

Eubacterium

Mogibacterium

Subdoligranulum

Anaerofilum

Rothia Dorea Acetanaerobacterium

Sedimentibacter

Oxobacter Lactococcus

Clostridium

Lactonifactor Bifidobacterium Odoribacter Escherichia/Shigella

Bifidobacterium

Coprobacillus

Sarcina Odoribacter

Weissella Lactobacillus

Phascolarctobacterium

Leuconostoc

Actinomyces

Coprococcus

Bacteroides

Ruminococcus Catenibacterium Roseburia Sutterella Butyricicoccus Dialister Anaerosporobacter

Pseudobutyrivibrio

Butyricicoccus

Sharpea

Blautia Faecalibacterium

Asaccharobacter

Blautia

Roseburia

Dialister

Veillonella

Sutterella

Streptococcus

Oribacterium

Anaerostipes

Actinobacillus Parasutterella

Actinobacillus

Moryella

Barnesiella

Figure 4 | Transition in microbiota composition across residence location is mirrored by changes in health indices. The PCoA plots show 8 groups of subjects defined by unweighted UniFrac microbiota analysis of community subjects (left), the whole cohort (centre), and long-stay subjects (right). The main circle shows the Wiggum plots corresponding to the 8 groups from whole-cohort analysis, in which disc sizes indicate genus over-abundance

relative to background. The pie charts show residence location proportions (colour coded as in Fig. 1c) and number of subjects per subject group. Curved arrows indicate transition from health (green) to frailty (red). FIM, functional independence measure; MNA, mini nutritional assessment; GDT, geriatric depression test; CC, calf circumference; CRP, C-reactive protein; IL, interleukin; BP, blood pressure; MMSE, mini-mental state examination.

182 | NATURE | VOL 488 | 9 AUGUST 2012