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Index

        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