Note: Page numbers of article titles are in boldface type.
A
Actinobacteria
in HIV infection, 739
in oral cancer, 715
Actinomyces, in oral cancer, 713
Adenocarcinoma, esophageal, 721–732
Alcohol, oral cancer and, 715–716
Anaerococcus
in HIV infections, 738
in vaginal microbiome, 750, 753
ATG16L1 gene, in Crohn disease, 766
Atropobium, in vaginal microbiome, 738–739, 750
Autophagy, in Crohn disease, 766
B
Bacterial vaginosis, 753–754
Bacteroides
in colorectal cancer, 702–704
in gut microbiome, 737
in HIV infection, 735, 737
in small bowel, 777
Bacteroidetes
in esophageal adenocarcinoma, 722
in HIV infection, 739
Barrett's esophagus
esophageal adenocarcinoma in, 722–728
proton pump inhibitors for, 774
Bifidobacterium
in colorectal cancer, 703
in HIV infection, 735
in small bowel, 777
in vaginal microbiome, 750
Bifidobacterium adolescentis SPM0212, in colorectal cancer, 705–706
Bile acids, in colorectal cancer, 704
Blautia, in colorectal cancer, 703
Brachyspira, in HIV infection, 737
Bulleidia, in vaginal microbiome, 754
C
Campylobacter, in HIV infection, 737
Candida
in HIV infection, 735–736
in vaginal microbiome, 749, 752
Capnocytophaga gingivalis, in oral cancer, 714
CARD15 gene, in Crohn disease, 765–766
Catenibacterium, in HIV infection, 737
Celiac disease, 777
Cervical microbiome, in HIV infection, 738–739
Chemokines, in colorectal cancer, 705
Chloroflexi, in HIV infection, 739
Cigarette smoking, oral cancer and, 715–716
Clavibacter, in oral cancer, 715
Clostridium
in colorectal cancer, 702
in Crohn disease, 765
in oral cancer, 713
in stomach, 775–776
Clostridium difficile infections
epidemiology of, 788
fecal microbiota transplantation for, 787–798
proton pump inhibitor effects on, 777–779
Colon, microbiome of, proton pump inhibitor effects on, 777–779
Colonoscopy, for fecal microbiota transplantation, 789–793
Colorectal cancer, 699–710
incidence of, 700–701
microbiota and
carcinogenesis and, 702–704
inflammation and, 704–705
normal population, 702
probiotic effects in, 705–706
molecular pathways in, 702
risk factors for, 701–702
Comamonadeaceae, in esophagus, 774
Coprococcus, in HIV infections, 738
Coriobacteriaceae, in vaginal microbiome, 753
Correa cascade, 775–776
Corynebacterium, in vaginal microbiome, 750
Crohn disease
colorectal cancer and, 702–705
gut microbiome and, 763–770
Cyanobacteria, in HIV infection, 739
Cytokines, in colorectal cancer, 705
D
Desulfomonoadaceae, in HIV infection, 739
Desulfovibrioaceae, in HIV infection, 739
Diet, colorectal cancer and, 702, 705–706
Dilaster, in vaginal microbiome, 754
DNA sequencing, for oral microbiota, 712
E
Enema, for fecal microbiota transplantation, 789–793
Enterobacteriaceae
in Crohn disease, 765
in HIV infection, 737
in oral cancer, 713
Enterococcus, in small bowel, 776–777
Enteropathy, in HIV infections, 736–738
Epithelial barrier integrity, maintenance of, in Crohn disease, 766
Escherichia
in Crohn disease, 765
in HIV infection, 737
Escherichia coli
in colorectal cancer, 702
in small bowel, 776–777
in vaginal microbiome, 749, 752
Esophageal adenocarcinoma, 721–732
microbiome in, 722–723, 728
normal microbiome and, 722
risk factors for, 721–722
Toll-like receptors in, 724–725
viruses in, 726–728
Esophagitis
esophageal adenocarcinoma in, 722–728
proton pump inhibitors for, 774
Esophagus, microbiome of, proton pump inhibitor effects on, 774–775
Eubacterium, in HIV infections, 738
Exiguobacterium oxidotolerans, in oral cancer, 714
F
Faecalibacterium, in colorectal cancer, 703
Familial adenomatous polyposis, 701
Fecal microbiota transplantation, 787–798
Firmicutes, in HIV infection, 736, 739
Fucosyltransferase 2, in Crohn disease, 766
Fusobacteriaceae, in HIV infection, 737
Fusobacterium
in colorectal cancer, 703
in esophageal adenocarcinoma, 722–723
in HIV infections, 738
in oral cancer, 713, 715
in rectal microbiome, 738
in vaginal microbiome, 755
G
Gardnerella, in vaginal microbiome, 738–739, 749–754
Gastric acid
production of, 772
proton pump inhibitors and, 771–785
Gastroesophageal reflux disease
esophageal adenocarcinoma in, 722–728
proton pump inhibitors for, 774
Gemella
in HIV infection, 736
in oral cancer, 714
Genetics, of Crohn disease, 763–770
Granulicatella, in HIV infection, 736
Granulicatella adiacens, in oral cancer, 714
Gut microbiomes
colorectal carcinogenesis and, 699–710
fecal microbiota transplantation and, 787–798
in Crohn disease, 763–770
in HIV infection, 736–738
proton pump inhibitors and, 771–785
H
Haemophilus, in oral cancer, 713
Helicobacter pylori, 711–712
in esophageal adenocarcinoma, 728
in esophagus, 774–775
in oral cancer, 714, 716
in small bowel, 777
in stomach, 775–776
Hereditary nonpolyposis colorectal cancer, 701–702
Human immunodeficiency virus infections, microbiome of, 733–745
action of, 734–735
cervical, 738–739
gut, 736–738
lung, 739–740
oral, 736
penile, 739
periodontal, 736
persistent immune activation and, 734
rectal, 738
vaginal, 738–739
Human Microbiome Project, 713, 747
Human Oral Microbe Identification Microarray, 712
Human papillomavirus, in esophageal adenocarcinoma, 726–728
I
Immunoproteomic analysis, for vaginal microbiome, 748
Inflammation, in colorectal carcinogenesis, 699–710
Inflammatory bowel disease
colorectal cancer and, 702–705
gut microbiome and, 763–770
International Human Microbiome Consortium, 713
J
Johnsonella ignava, in oral cancer, 714
K
Klebsiella pneumoniae, in small bowel, 776–777
L
Lachnospiraceae
in esophagus, 774
in HIV infection, 736, 738
Lactobacillus
in colon, 779
in colorectal cancer, 705–706
in gut microbiome, 737
in HIV infection, 735–739
in oral microbiome, 736
in small bowel, 777
in stomach, 775–776
in vaginal microbiome, 738–739, 749–755
Lung microbiome, in HIV infection, 739–740
M
Megasphaera, in vaginal microbiome, 753–754
Metabolomic/lipidomic analyses, for vaginal microbiome, 748
Metagenomic sequencing, for oral microbiota, 712
Metatranscriptomic analysis, for vaginal microbiome, 748
Methylobacteriaceae, in esophagus, 774
Microbial-associated molecular patterns, in Crohn disease, 765–766
Microbiomes
esophageal, 721–732
gut
colorectal carcinogenesis and, 699–710
fecal microbiota transplantation and, 787–798
in Crohn disease, 763–770
proton pump inhibitors and, 771–785
in human immunodeficiency virus infections, 733–745
oral, 711–719
vaginal, 738–739, 747–761
Micrococcus, in oral cancer, 714
Mobiluncus, in vaginal microbiome, 750, 753, 755
Mogibacterium
in colorectal cancer, 703
in HIV infection, 737
Multi-Omnic Microbiome Study-Pregnancy Initiative, 748
Mycoplasma, in vaginal microbiome, 753–755
N
Nasogastric tubes, for fecal microbiota transplantation, 789–793
Neisseria, in esophageal adenocarcinoma, 723
Neisseria gonorrhea, in vaginal microbiome, 749–750
NOD2 gene, in Crohn disease, 765–766
O
Oral cancer, microbiome and, 711–719
carcinogenesis mechanisms and, 715–716
culture-based studies of, 713–714
methods for detection, 712
molecular-based studies of, 714–715
normal, 713
Oral microbiome, in HIV infection, 736
P
Parvimonas, in vaginal microbiome, 754
Pasteurella, in Crohn disease, 765
Penile microbiome, in HIV infection, 739
Peptoniphilus, in vaginal microbiome, 750
Peptostreptococcus
in HIV infections, 738
in vaginal microbiome, 753
Periodontal microbiome, in HIV infection, 736
Pneumonia, in HIV infection, 739–740
Porphyromonas
in colorectal cancer, 703
in HIV infection, 736, 738
in oral cancer, 713, 715
Pregnancy, vaginal microbiome in, 754–755
Preterm birth, vaginal microbiome in, 754–755
Prevotella
in colorectal cancer, 703
in esophageal adenocarcinoma, 723
in HIV infection, 735, 737–738
in oral cancer, 713–715
in vaginal microbiome, 738, 749–750, 753–754
Probiotics, in colorectal cancer, 705–706
Propionibacterium, in vaginal microbiome, 750
Proteobacteria
in esophageal adenocarcinoma, 722
in HIV infection, 736
Proton pump inhibitors, 771–785
mechanism of action of, 772–774
microbiome effects of, 774–779
Pseudomonas aeruginosa
in HIV infection, 735, 739
in lung microbiome, 739
in vaginal microbiome, 749
Pseudomonas fluorescens, in HIV infection, 737
R
Ralstonia, in oral cancer, 715
Rectal microbiome, in HIV infection, 738
Reflux esophagitis
esophageal adenocarcinoma in, 722–728
proton pump inhibitors for, 774
Ribosomal Database Project, 713
Roseburia, in HIV infections, 738
Rothia, in oral cancer, 715
Ruminococcus, in HIV infections, 738
S
16S rRNA gene surveys, for vaginal microbiome, 748
Salmonella typhi, in oral cancer, 716
Sarcina, in HIV infection, 736
Selenomonas, in HIV infection, 736
Shigella, in Crohn disease, 765
Small bowel, microbiome of, proton pump inhibitor effects on, 776–777
Smoking, oral cancer and, 715–716
Sneathia, in vaginal microbiome, 750, 753, 755
Sphingomonas, in oral cancer, 715
Spirochaetes, in esophageal adenocarcinoma, 722
Squamous cell carcinoma, oral, 711–719
Staphylococcus, in HIV infection, 736
Staphylococcus aureus
in oral cancer, 714
in vaginal microbiome, 749
Stomach, microbiome of, proton pump inhibitor effects on, 775–776
Stool transplantation, for Clostridium difficile infections, 787–798
Streptococcus
in esophageal adenocarcinoma, 722
in esophagus, 774
in HIV infection, 736
in oral cancer, 713–716
in oral microbiome, 736
in stomach, 775–776
in vaginal microbiome, 749
Streptococcus anginosus, in oral cancer, 714
Streptococcus bovis
in colorectal cancer, 702–703
in oral cancer, 716
Streptococcus mitis, in oral cancer, 714
Symbiotic mutualism, 700
T
T cells, regulatory, in HIV infection, 735
Tobacco use, oral cancer and, 715–716
Toll-like receptors, in esophageal adenocarcinoma, 724–725
Transplantation, fecal microbiota, 787–798
Tropheryma whipplei, in HIV infection, 740
U
Ulcerative colitis, colorectal cancer and, 702–705
Ureaplasma, in vaginal microbiome, 753, 755
V
Vaginal microbiome, 747–761
factors influencing, 750–752
genetic factors in, 750–751
healthy organisms dominating, 749–750
in bacterial vaginosis, 753–754
in disease states, 752–754
in HIV infection, 738–739
in pregnancy, 754–755
in preterm birth, 754–755
study methods for, 748
Vaginal Microbiome Consortium, 748
Vancomycin, for Clostridium difficile infections, 790
Veillonella
in Crohn disease, 765
in esophageal adenocarcinoma, 723
in HIV infection, 736
in oral cancer, 713–714
Virginia Commonwealth University, Vaginal Microbiome Consortium, 748
Viridans streptococci, in oral cancer, 716
Viruses, in esophageal adenocarcinoma, 726–728
W
Whipple disease, 740
Whole genome sequencing, for vaginal microbiome, 748
Whole metagenomic shotgun sequencing, for vaginal microbiome, 748
