Profiling the human intestinal environment under physiological conditions.

The spatiotemporal structure of the human microbiome, proteome and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion.

Short-Term Dairy Product Elimination and Reintroduction Minimally Perturbs the Gut Microbiota in Self-Reported Lactose-Intolerant Adults.

An outstanding question regarding the human gut microbiota is whether and how microbiota-directed interventions influence host phenotypic traits. Here, we employed a dietary intervention to probe this question in the context of lactose intolerance. To assess the effects of dietary dairy product elimination and (re)introduction on the microbiota and host phenotype, we studied 12 self-reported mildly lactose-intolerant adults with triweekly collection of fecal samples over a 12-week study period: 2 weeks of baseline diet, 4 weeks of dairy product elimination, and 6 weeks of gradual whole cow milk (re)introduction.

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression.

Microbial biogeography and ecology of the mouth and implications for periodontal diseases.

In humans, the composition of microbial communities differs among body sites and between habitats within a single site. Patterns of variation in the distribution of organisms across time and space are referred to as "biogeography." The human oral cavity is a critical observatory for exploring microbial biogeography because it is spatially structured, easily accessible, and its microbiota has been linked to the promotion of both health and disease.

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.

Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be induced using a clinically-relevant iso-osmotic agent. We designed and executed such a disturbance in human volunteers using a dense longitudinal sampling scheme extending before and after induced diarrhea.

Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States.

Background: Our current understanding of the composition and stability of the human distal gut microbiota is based largely on studies of infants and adults living in developed countries. In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries.

Methodology/principal Findings: We compared the diversity, composition, and temporal stability of the fecal microbiota of healthy children, ages 9 to 14 years, living in an urban slum in Bangladesh with that of children of the same age range in an upper-middle class suburban community in the United States.

The application of ecological theory toward an understanding of the human microbiome.

The human-microbial ecosystem plays a variety of important roles in human health and disease. Each person can be viewed as an island-like "patch" of habitat occupied by microbial assemblages formed by the fundamental processes of community ecology: dispersal, local diversification, environmental selection, and ecological drift. Community assembly theory, and metacommunity theory in particular, provides a framework for understanding the ecological dynamics of the human microbiome, such as compositional variability within and between hosts.

Comparisons of distance methods for combining covariates and abundances in microbiome studies.

This article compares different methods for combining abundance data, phylogenetic trees and clinical covariates in a nonparametric setting. In particular we study the output from the principal coordinates analysis on UNIFRAC and WEIGHTED UNIFRAC distances and the output from a double principal coordinate analyses DPCOA using distances computed on the phylogenetic tree. We also present power comparisons for some of the standard tests of phylogenetic signal between different types of samples.

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.

The indigenous human microbiota is essential to the health of the host. Although the microbiota can be affected by many features of modern life, we know little about its responses to disturbance, especially repeated disturbances, and how these changes compare with baseline temporal variation. We examined the distal gut microbiota of three individuals over 10 mo that spanned two courses of the antibiotic ciprofloxacin, analyzing more than 1.

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process.

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.

The human intestinal microbiota is essential to the health of the host and plays a role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses. Antibiotics may disrupt these coevolved interactions, leading to acute or chronic disease in some individuals. Our understanding of antibiotic-associated disturbance of the microbiota has been limited by the poor sensitivity, inadequate resolution, and significant cost of current research methods.

An ecological and evolutionary perspective on human-microbe mutualism and disease.

The microbial communities of humans are characteristic and complex mixtures of microorganisms that have co-evolved with their human hosts. The species that make up these communities vary between hosts as a result of restricted migration of microorganisms between hosts and strong ecological interactions within hosts, as well as host variability in terms of diet, genotype and colonization history. The shared evolutionary fate of humans and their symbiotic bacteria has selected for mutualistic interactions that are essential for human health, and ecological or genetic changes that uncouple this shared fate can result in disease.

Performance of the translational apparatus varies with the ecological strategies of bacteria.

Protein synthesis is the predominant activity of growing bacteria; the protein synthesis system accounts for more than one-half the cell's dry mass and consumes most of the cell's energy during rapid growth. Translation has been studied extensively using model organisms, and the translational apparatus is qualitatively similar in terms of structure and function across all known forms of life. However, little is known about variation between organisms in translational performance.

Assembly of the human intestinal microbiota.

Complex microbial ecosystems occupy the skin, mucosa and alimentary tract of all mammals, including humans. Recent advances have highlighted the tremendous diversity of these microbial communities and their importance to host physiology, but questions remain about the ecological processes that establish and maintain the microbiota throughout life. The prevailing view, that the gastrointestinal microbiota of adult humans is a climax community comprised of the superior competitors for a stable set of niches, does not account for all of the experimental data.

Diversity of the human intestinal microbial flora.

The human endogenous intestinal microflora is an essential "organ" in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms.

Differences in codon bias cannot explain differences in translational power among microbes.

Background: Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons.

Characterization of camptothecin-resistant Chinese hamster lung cells.

Three camptothecin-resistant sublines (V79r, IRS-1r and IRS-2r) of V79 cells and their irradiation-sensitive mutants, IRS-1 and IRS-2, were developed by stepwise, continuous exposure to camptothecin (CPT). The degree of resistance varied among these cells. Based on the biochemical characterizations of these resistant cell lines, the mechanisms which could be responsible for the resistance to CPT were proposed to be: (a) a decrease in the intracellular accumulation of CPT with or without alteration of DNA topoisomerase I, (b) a decrease in the amount of DNA topoisomerase I, or (c) a decrease in the sensitivity of DNA topoisomerase I to CPT.

Poly(ADP-ribose) metabolism in proliferating versus quiescent cells and its relationship to their radiation responses.

In the murine tumour cell lines 66 and 67 growing in vitro, quiescent (Q; unfed plateau-phase) cells are more sensitive to X-ray-induced cell killing than are proliferating (P) cells, while St4 cells (Q cells that have been re-fed and returned to 37 degrees C for 4h) are similar to P cells in radiosensitivity. We have been investigating parameters of poly(ADP-ribose) metabolism in order to determine whether such factors contribute to the variations in radiosensitivity of these growth states. These parameters were cellular NAD content, the activity of poly(ADP-ribose) transferase (ADPRT) in permeabilized cells and the activity of poly(ADP-ribose)-degrading enzymes.

Nuclear thiols: technical limitations on the determination of endogenous nuclear glutathione and the potential importance of sulfhydryl proteins.

Significant discrepancies were found between the values for glutathione levels determined by the Tietze enzymatic assay and those measured by labeling with monobromobimane followed by HPLC analysis when these methods were applied to proliferating and quiescent cells of the 66 murine mammary tumor line depleted of glutathione by buthionine sulfoximine or to nuclei prepared from these cells by permeabilization with Nonident detergent. The probable origin of the discrepancy was traced to the presence of acid-soluble sulfhydryl proteins in the extracts which are thought to lead to erroneous values in the Tietze assay method. Using the monobromobimane-HPLC method it was found that the low-molecular-weight thiol levels in nuclei prepared by detergent permeabilization equilibrate in less than 1 min with the permeabilizing medium, indicating that (i) endogenous nuclear glutathione levels cannot be determined reliably using conventional methods of cellular disruption and (ii) the endogenous nuclear glutathione level is likely to be the same as the cytoplasmic value.

The physiological state as a modifier of radiation-induced cytotoxicity in heterogeneous murine tumor cells growing in vitro.

The oxic radiation response (cytotoxicity) of two heterogeneous murine tumor-cell lines cultured in vitro was studied as a function of the cell's physiological state at the time of X-irradiation. The proliferating (P) 66 and 67 cells displayed equal radiosensitivities; however, the quiescent (Q) cells were considerably more radiosensitive than the P cells, and the 66Q cells were even more radiosensitive than the 67Q cells. Also, the 66Q cells continued to proliferate slowly with about 85 per cent in the G1 phase and 10 per cent in the S phase, while the 67 Q cells displayed a more complete G1 arrest (92-95 per cent).

Repair of DNA single- and double-strand breaks in proliferating and quiescent murine tumor cells.

We evaluated the relationship between the repair of DNA single- and double-strand breaks and cellular radiosensitivity in proliferating vs. quiescent cells of the mouse mammary tumor lines 66 and 67 in vitro, using the technique of filter elution at pH 12.2, pH 7.

Cell cycle effect on the induction of DNA double-strand breaks by X rays.

Filter elution was used to compare X-ray-induced DNA single- and double-strand breaks in proliferating (P) and quiescent (Q) cells of the 66 and 67 mouse mammary tumor lines. There was no difference either between cell type or between growth states in the amount of single-strand breaks as defined by elution at pH 12.2.

Toxic effects of acute glutathione depletion by buthionine sulfoximine and dimethylfumarate on murine mammary carcinoma cells.

Glutathione (GSH) depletion to approximately equal to 5% of control for 48 h or longer by 0.05 mM L-buthionine sulfoximine (BSO) led to appreciable toxicity for the 66 murine mammary carcinoma cells growing in vitro [L.A.

Endogenous thiol levels in heterogeneous murine tumor cells as a function of the physiological state and the response to X-irradiation.

The endogenous thiols (PSH, protein sulfhydryls; NPSH, nonprotein sulfhydryls; and GSH, glutathione) were measured in the 66 and 67 murine carcinoma cells growing under different physiological conditions in vitro (e.g., proliferation, P; nutrient-deprived quiescence QI; and QI cells stimulated by refeeding the monolayer in situ and assayed 4 (St4) and 14 (St14) h later).