Faculty Bibliography

Understanding of the human microbiome continues to grow rapidly; however, reports on changes in the microbiome after HIV infection are still limited. This review surveys the progress made in methodology associated with microbiome studies and highlights the remaining challenges to this field. Studies have shown that commensal oral, gut, vaginal, and penile bacteria are vital to the health of the human immune system. Our studies on crosstalk among oral and gastrointestinal soluble innate factors, HIV, and microbes indicated that the oral and gut microbiome was altered in the HIV-positive samples compared to the negative controls. The importance of understanding the bacterial component of HIV/AIDS, and likelihood of "crosstalk" between viral and bacterial pathogens, will help in understanding the role of the microbiome in HIV-infected individuals and facilitate identification of novel antiretroviral factors for use as novel diagnostics, microbicides, or therapeutics against HIV infection.

Rationale: Partial seizures in temporal lobe epilepsy (TLE) are classified as complex-partial, resulting in a loss of consciousness, or simple-partial, associated with preserved consciousness. The mechanistic underpinnings of impaired consciousness in partial seizures are poorly understood. Investigators have previously suggested that unconsciousness during partial seizures may be related to bilateral temporal lobe involvement, seizure onset in the language-dominant hemisphere, or increased cortico-thalamic synchrony. Earlier work has indeed shown that temporal lobe seizures are often associated with bilateral slow rhythms and decreased cerebral blood flow in the frontoparietal neocortex. Ictal neocortical slow rhythms resemble cortical activity observed during sleep or deep anesthesia. However, no prior investigations have directly examined the relationship between ictal neocortical slow activity and behavioral unresponsiveness. Methods: We analyzed intracranial electroencephalographic (EEG) recordings during 63 partial seizures in 26 TLE patients. Blinded reviewers analyzed behavioral responsiveness based on video recordings of seizures and classified consciousness as impaired (complex-partial) or unimpaired (simple-partial). Results: We found significantly elevated delta-range 1-2 Hz slow activity in the frontal and parietal neocortices during complex-partial compared to simple-partial seizures. Also, fast beta-range EEG activity in the contralateral temporal lobe, indicating seizure propagation, was significantly correlated with slow delta activity in the frontoparietal neocortex. Furthermore, we observed that seizure onset in the languagedominant hemisphere and bilateral temporal lobe involvement were more common during complex- than simple-partial seizures. Conclusions: We have proposed a 'network inhibition hypothesis' based on prior human and animal studies, in which subcortical arousal systems are disrupted by partial seizures, producing a depressed cortical state of slow activity and impaired consciousness. Our present findings illustrate that impaired consciousness is associated with ictal neocortical slow and bilateral temporal fast rhythms, raising the possibility that spread of seizure activity to bilateral temporal lobes may exert a powerful inhibitory effect on subcortical arousal networks. Further investigations are necessary to fully determine the role of cortical-subcortical networks in ictal neocortical dysfunction, and may ultimately lead to specific treatments targeted at preventing this negative consequence of TLE

Objectives: To determine if cigarette smoking and oral squamous cell carcinoma (OSCC) are associated with an alteration of the oral microbiome, and to determine if the oral microbiome is capable of activating cigarette carcinogens. Methods: Oral wash samples were collected from 9 patients with OSCC and 10 non-cancer controls (including 5 smokers and 5 non-smokers). Bacterial DNA was isolated from each oral wash and then 16S rRNA gene survey performed by 454 pyrosequencing of the V3-5 region to identify bacterial sequences present in oral wash samples. Bacterial sequences present in OSCC patient samples and in control patient samples were then categorized. Also, a mock community, composed of 5 bacterial species found in the oral microbiome, was tested for its ability to metabolize cigarette carcinogens. Results: Samples of the oral microbiome were classified into type I and type II microbiomes, based on taxonomic similarity between samples. The type I microbiome was dominated by Grampositive bacteria whereas the type II microbiome was dominated by Gram-negative bacteria. Non-cancer control patients had the type I microbiome (9/10). In contrast, OSCC patients had the type II microbiome (6/9). Furthermore, OSCC was associated with an apparent decrease in the relative abundance of Streptococcus (22.3%) compared with non-smoking (39.4%) and smoking controls (40.1%). There was a step-wise increase in the relative abundance of Veilonella along the non-smoking controls (2.3%) -> smoking controls (6.8%) -> OSCC (9.9%) sequence. Metabolomic analysis demonstrated that a mock bacterial community composed of Streptococcus mitis and Veilonella dispar was able to hydroxylate N-nitrosodieth-ylamine and degrade p-chloroaniline, both being carcinogens found in cigarette smoke. Conclusions: Cigarette smoking and oral squamous cell carcinoma are associated with an alteration of the oral microbiome. The oral microbiome has the potential to modulate oral cancer risk by activating cigarette carcinogens

OBJECTIVES: The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. METHODS: Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. RESULTS: The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70 approximately 0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84). CONCLUSION: Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.

AIM: To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome. METHODS: A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species. Candidate primers evaluated were from the European rRNA database. To assess the effect of sequence length on accuracy of classification, 16S rRNA genes of various lengths were created by trimming the full length sequences. Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs. The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP). The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes, represented by 36 phyla. RESULTS: Truncation to 100 nucleotides (nt) downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87 (39.7%) of the 219 sequences, compared with misclassification of only 29 (13.2%) sequences with truncation to 350 nt. Among 350-nt sequence reads within various regions of the 16S rRNA gene, the reverse read of an amplicon generated using the 343F/798R primers had the least (8.2%) effect on classification. In comparison, truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0% of the 219 sequences. The 343F/798R amplicon accurately assigned 91.8% of the 219 sequences at the species level. Weighted by abundance of the species in the esophageal dataset, the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage (92%). Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species. Assuming that a typical polymerase chain reaction can tolerate 2 mismatches between a primer and a template, the modified 347F and 803R primers should be able to anneal 98% and 99.6% of all 16S rRNA genes in the RDP database. CONCLUSION: 347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes.

We report the first case of adult meningitis confirmed to be due to Streptococcus gallolyticus subsp. pasteurianus. Phenotypically reported as Streptococcus bovis biotype II/2, 16S rRNA sequencing revealed S. gallolyticus subsp. pasteurianus. Because of taxonomic uncertainties, S. gallolyticus subsp. pasteurianus may be an underrecognized agent of systemic infections

Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 +/- 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% +/- 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2 degrees structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in "Candidatus Protochlamydia amoebophila." Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.

BACKGROUND & AIMS: Gastroesophageal reflux causes inflammation and intestinal metaplasia and its downstream sequelum adenocarcinoma in the distal esophagus. The incidence of esophageal adenocarcinoma has increased approximately 6-fold in the United States since the 1970s, accompanied with a significant increase in the prevalence of gastroesophageal reflux disease (GERD). Despite extensive epidemiologic study, the cause for GERD and the unexpected increases remain unexplainable. Microbes are among the environmental factors that may contribute to the etiology of GERD, but very little research has been done on the esophageal microbiome, particularly in its relation to GERD. This is the first comprehensive reported correlation between a change in the esophageal microbiome and esophageal diseases. METHODS: Biopsy samples of the distal esophagus were collected from 34 patients. Host phenotypes were histologically defined as normal, esophagitis, or Barrett's esophagus (intestinal metaplasia). Microbiomes from the biopsy samples were analyzed by bacterial 16S ribosomal RNA gene survey and classified into types using unsupervised cluster analysis and phenotype-guided analyses. Independence between host phenotypes and microbiome types were analyzed by Fisher exact test. RESULTS: Esophageal microbiomes can be classified into 2 types. The type I microbiome was dominated by the genus Streptococcus and concentrated in the phenotypically normal esophagus. Conversely, the type II microbiome contained a greater proportion of gram-negative anaerobes/microaerophiles and primarily correlated with esophagitis (odds ratio, 15.4) and Barrett's esophagus (odds ratio, 16.5). CONCLUSIONS: In the human distal esophagus, inflammation and intestinal metaplasia are associated with global alteration of the microbiome. These findings raise the issue of a possible role for dysbiosis in the pathogenesis of reflux-related disorders