ARTICLE RESEARCH
Colour key
4A 3A 3B 4B 1A 2A 1B 2B
a
c
–3 –1 1 3
Bacteroidaceae Rikenellaceae Porphyromonadaceae Prevotellaceae Marinilabiaceae Ruminococcaceae Lachnospiraceae Incertae Sedis XIV Eubacteriaceae Clostridiaceae Erysipelotrichaceae Alcaligenaceae Bifidobacteriaceae Other Unclassified
PC1 (6.7%)
b
100
50
PC1 (23%)
0
community-dwelling subjects. Eighteen other non-UniFrac b -diversity metrics supported microbiota separation by residence location (Supplementary Fig. 1). When we examined OTU abundance, we identified a cluster com- prised of the majority of the long-stay subjects, separated from the majority of the community-dwelling and young healthy subjects (Fig. 1c). Family-level microbiota assignments showed that long-stay microbiota had a higher proportion of phylum Bacteroidetes , compared to a higher proportion of phylum Firmicutes and unclassified reads in community-dwelling subjects (Fig. 1c). At genus level, Coprococcus and Roseburia (of the Lachnospiraceae family) were more abundant in the faecal microbiota of community-dwelling subjects (Supplementary Table 1 shows complete list of genera differentially abundant by com- munity location). Genera associated with long-stay subjects included Figure 1 | Microbiota analysis separates elderly subjects based upon where they live in the community. a , Unweighted and b , weighted UniFrac PCoA of faecal microbiota from 191 subjects. Subject colour coding: green, community; yellow, day hospital; orange, rehabilitation; red, long-stay; and purple, young healthy control subjects. c , Hierarchical Ward-linkage clustering based on the Spearman correlation coefficients of the proportion of OTUs, filtered for OTU subject prevalence of at least 20%. Subjects colour coding as in a . Labelled
Parabacteroides , Eubacterium , Anaerotruncus , Lactonifactor and Coprobacillus (Supplementary Table 2). The genera associated with community belonged to fewer families, Lachnospiraceae were the most dominant. Thus, the microbiota composition of an individual segre- gated depending on where they lived within a single ethnogeographic region, in a homogeneous cohort where confounding effects of climate, culture, nationality and extreme environment were not a factor. Concordance of diet and microbiota Dietary data (for 168 of the 178 subjects, plus five percutaneous endoscopic gastrostomy (PEG)-fed subjects) was collected through a semiquantitative, 147-item, food frequency questionnaire (FFQ), weighted by 10 consumption frequencies. The data were visualized with correspondence analysis (CoA; Fig. 2a). The first CoA axis clusters in top of panel c (basis for the eight groups in Fig. 4) are highlighted by black squares. OTUs are clustered by the vertical tree, colour-coded by family assignments. Bacteroidetes phylum, blue gradient; Firmicutes , red; Proteobacteria , green; and Actinobacteria , yellow. Only 774 OTUs confidently classified to family level are visualized. The bottom panel shows relative abundance of family-classified microbiota.
a
Colour key
b
c
Unweighted UniFrac
–3–2–10 1 2 3
PC1
Weighted UniFrac
Non-mineral/vitamin supp.
Vitamin supp.
Herbal tea
Dairy desserts
Porridge
Milk
Probiotic yoghurt
Mineral supp.
Spinach
Wheat-free bread
Brown rice
Chicken
Dried fruit
Mashed potatoes
Garlic Sweet peppers
Oily fish
Milk pudding
Wine
Fried fish
White fish
Low-fat milk
Boiled potatoes
Sugar
Citrus fruit
Onions
Processed meat
Cheese
Coffee
Sweets
Tomatoes
Plain buiscuits
Jam
Butter
Choc. biscuits
White bread
PC1
DG1
DG2
DG3
DG4
Figure 2 | Dietary patterns in community location correlate with separations based on microbiota composition. a , Food correspondence analysis. Top panel, FFQ PCA; bottom panel, driving food types. b , Procrustes analysis combining unweighted and weighted UniFrac PCoA of microbiota (non-circle end of lines) with food type PCA (circle-end of lines). c , Four dietary groups (DG1, DG2, DG3 and DG4) revealed through complete linkage clustering using Euclidean distances applied to first eigenvector in
correspondence analysis. Colour codes in a , and horizontal clustering in b and c , are community location, as per Fig. 1. Food labelling in lower panel in a , and vertical clustering in c : green, fruit and vegetables; orange, grains such as potatoes, cereals and bread; brown, meat; cyan, fish; yellow, dairy products; blue, sweets, cakes and alcohol; grey vitamins, minerals and tea. Only peripheral and most driving foods are labelled; for a complete list see Supplementary Table 2.
9 AUGUST 2012 | VOL 488 | NATURE | 179
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