Table 2. Human studies of the gut microbiota and C. difficile infection.

Sample collection	Microbiome analysis	Structural changes to the gut microbiota	Reference
Fecal samples were collected from three subject groups: healthy young adults, aged 21–34 y (n = 7); healthy elderly people, aged 67–88 y (n = 4); and elderly patients with C. difficile associated diarrhea (CDAD), aged 67–73 years (n = 4).	Characterization of cellular fatty acid (CFA) profiles	•      CDAD patients had a greater diversity of facultative species, Lactobacilli and Clostridia, and reduced numbers of Bacteroides, Prevotella and Bifidobacteria. •      Enterobacteria and Enterococci increased in CDAD patients.	91
Fecal samples of patients with CDAD (both initial and recurrent episodes) were obtained from 10 individuals—patients with CDAD (n = 7) (initial C. difficile, ICD n = 3 and recurrent C. difficile, RCD n = 4) and control subjects (n = 3).	16S rRNA-encoding gene clone libraries	•      Species richness in the patients with ICD was similar to the controls. •      Species richness in the RCD patients was consistently lower than both the patients with ICD and the controls. •      RCD is associated with decreased overall diversity of the gut microbiota.	93
Fecal samples from 599 patients, hospitalized from September 2006 through May 2007 in Montreal, Quebec, were obtained within 72 h after admission. Twenty-five developed CDAD, and 50 matched controls were selected for analysis.	16S rRNA-gene encoding microarrays	•      Probe intensities were higher for Firmicutes, Proteobacteria, and Actinobacteria in CDAD patients, compared with controls, whereas probe intensities for Bacteroidetes were lower. •      After epidemiologic factors were controlled for, only Bacteroidetes and Firmicutes remained significantly and independently associated with development of CDAD.	90
Fecal samples were collected from elderly subjects recruited from the community; including outpatient, short-term respite, and long-term hospital stay subjects. The carriage rate for C. difficile ranged from 1.6% (n = 123) for subjects in the community, to 9.5% (n = 43) in outpatient settings, and increasing to 21% (n = 151) for patients in short- or long-term care in hospital.	Culture-independent Roche/454 pyrosequencing (V4 region)	•      C. difficile positive subjects had a decrease in Enterococcaceae but an increase in Lactobacillaceae and Enterobacteriaceae. •      The dominant 072 ribotype was carried by 43% (12/28) of subjects, while the hypervirulent strain R027 (B1/NAP1/027) was isolated from 3 subjects (11%), 2 of whom displayed CDAD symptoms at the time of sampling. •      Emerging ribotypes (078 and 018) were also isolated from two asymptomatic subjects.	89
Fecal samples (n = 208), of which 171 were routine samples and 37 were from healthy volunteers were collected. Of the 171 routine samples, 105 were C. difficile positive and 66 were C. difficile negative. From all 105 positive fecal samples C. difficile was isolated and strains were assigned to 22 different C. difficile PCR ribotypes. The five most frequent ribotypes were 027, 014/020, 081, 002 and 023.	Denaturing high-pressure liquid chromatography (DHPLC) and machine learning methods	•      C. difficile positive samples showed lower levels of bacterial taxons from Bifidobacterium longum, Prevotella sp. and Bacteroides sp.. •      Bifidobacterium longum was the most important predictor for the C. difficile negative status. •      C. difficile positive samples had increases in Ruminococcus bromii, the family Peptostreptococcaceae and Streptococcus sp./Enterococcus sp. 2. •      Healthy donors had higher frequencies of Methanobrevibacter smithii compared with C. difficile negative samples sent for routine testing and to C. difficile positive samples.	92
Fecal samples were collected from fecal microbiota transplant patients or FMT (n = 3) and their healthy donors (n = 3).	High-throughput 16S rRNA gene sequencing (V6 region)	•      Post FMT samples from patients showed an increase in the abundance of Firmicutes and Bacteroidetes. Proteobacteria and Actinobacteria were less abundant (< 5%) than that found in patients prior to FMT. •      Bacteroidetes phylum was represented by family members Bacteroidaceae, Rikenellaceae and Porphyromonadaceae, and were largely comprised of Bacteroides, Alistipes and Parabacteroides genera. •      -Firmicutes phylum was represented by family members Ruminococcaceae, Lachnospiraceae, Verrucomicrobiaceae and unclassified Clostridiales and members of the Firmicutes.	96
Fecal samples were collected from individuals with C. difficile infection (CDI) (n = 39), subjects with nosocomial diarrhea not attributed to C. difficile (CDN) group (n = 36), and healthy controls (n = 40).	Culture-independent Roche/454 pyrosequencing (V1-V3 primers)	•      CDI and CDN subjects were accompanied by a marked decrease in microbial diversity and species richness driven by a decrease in phylotypes within the Firmicutes phylum. •      CDI and CDN subjects were depleted of Ruminococcaceae and Lachnospiraceae family members and butyrate-producing C2-C4 anaerobic fermenters.	88