Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Selective detection of cysteine and glutathione using gold nanorods

A unique strategy for the selective detection of micromolar concentrations of cysteine/glutathione in the presence of various other α -amino acids through the plasmon coupling of Au nanorods is reported

Gold nanorods to nanochains: mechanistic investigations on their longitudinal assembly using α,ω -alkanedithiols and interplasmon coupling

Mechanistic investigations on the end-to-end assembly of Au nanorods to nanochains, in the presence of α,ω -alkanedithiols, were reported. A decrease in the longitudinal plasmon absorption was observed along with a concomitant formation of a new red-shifted band above a critical concentration of dithiol, which is attributed to the interplasmon coupling in assembled nanorods. However, no noticeable spectral changes were observed below the critical concentration, and the TEM studies indicate that the nanorods remain isolated and randomly distributed. This step is ascribed as an incubation step wherein one of the thiol groups of α,ω -alkanedithiol preferentially binds onto the edges of the nanorods, leaving the other thiol group free. Above the critical concentration, a chain up process proceeds through the interlocking of nanorods, initially to dimers and subsequently to oligomers, which results in longitudinal interplasmon coupling. The dimerization step follows second-order kinetics which deviates with time due to oligomerization. The rate constants for dimerization of nanorods possessing various dithiols and their energy of activation were determined. The large activation energy for the dimerization further confirms that the process is not diffusion but activation controlled

Framework and Overview of a State-Wide College Mental Health Program in Kerala, India

Background: Mental health issues are common among college students, and structured services have been proven to enhance outcomes. Despite increased enrolment for higher education in India, college mental health services remain sparse. JEEVANI is the first structured state-wide college mental health service in India. This paper describes its framework and provides an overview of its functioning during the initial five months. Methods: In 2019–2020, the Directorate of Collegiate Education, Government of Kerala, implemented the program in 66 colleges catering to approximately 60,000 students. Qualified counsellors were trained to identify issues and provide interventions and early referrals, using a stepped-care approach. They conducted awareness programs to promote mental health and reduce stigma. Results: The services were accessed by 2,315 students during the assessment period (October 2019 to February 2020). The beneficiaries were predominantly females (54.1%). Over a third (38.8%) belonged to the lower socio-economic strata, and 2.5% had significant vulnerabilities. Although no syndromal diagnoses were made, anxiety and depression were the most common presentations. The counsellors provided 3,758 individual sessions and facilitated support for students who reported academic difficulties or interpersonal issues. Severe mental illness was detected in 54 students, and referrals for specialist mental health input were initiated in 68. Conclusion: Describing the framework, sharing the technical material, and providing an overview of its functioning from a resource-constrained setting in India may encourage higher education institutions in low- and middle-income countries to consider similar projects

Plant diversity enhances ecosystem responses to elevated CO2 and nitrogen deposition

http://www.nature.com/natureHuman actions are causing declines in plant biodiversity, increases in atmospheric CO2 concentrations and increases in nitrogen deposition; however, the interactive effects of these factors on ecosystem processes are unknown1, 2. Reduced biodiversity has raised numerous concerns, including the possibility that ecosystem functioning may be affected negatively1, 2, 3, 4, which might be particularly important in the face of other global changes5, 6. Here we present results of a grassland field experiment in Minnesota, USA, that tests the hypothesis that plant diversity and composition influence the enhancement of biomass and carbon acquisition in ecosystems subjected to elevated atmospheric CO2 concentrations and nitrogen deposition. The study experimentally controlled plant diversity (1, 4, 9 or 16 species), soil nitrogen (unamended versus deposition of 4 g of nitrogen per m2 per yr) and atmospheric CO2 concentrations using free-air CO2 enrichment (ambient, 368 micromol mol-1, versus elevated, 560 micromol mol-1). We found that the enhanced biomass accumulation in response to elevated levels of CO2 or nitrogen, or their combination, is less in species-poor than in species-rich assemblages

Aligned Growth of Gold Nanorods in PMMA Channels: Parallel Preparation of Nanogaps

We demonstrate alignment and positional control of gold nanorods grown in situ on substrates using a seed-mediated synthetic approach. Alignment control is obtained by directing the growth of spherical nanoparticle seeds into nanorods in well-defined poly(methyl methacrylate) nanochannels. Substrates with prepatterned metallic electrodes provide an additional handle for the position of the gold nanorods and yield nanometer-sized gaps between the electrode and nanorod. The presented approach is a novel demonstration of bottom-up device fabrication of multiple nanogap junctions on a single chip mediated via in situ growth of gold nanorods acting as nanoelectrodes