Defining Microbiome Health through a Host Lens.

We are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state. The specifics of this entanglement remain largely unknown and are somewhat unique to individuals, and when any one piece of this complex system breaks, our health can suffer. There appear to be many ways to build a healthy, functional microbiome and several distinct ways in which it can break. Despite the hundreds of associations with human disease, there are only a handful of cases where the exact contribution of the microbiome to the etiology of disease is known. Our laboratory takes a systems approach, integrating dynamic high-throughput host phenotyping with eco-evolutionary dynamics and metabolism of gut microbiota to better define health and disease for each individual at the ecosystem level

Microbial diversity - exploration of natural ecosystems and microbiomes

© The Author(s), 2015. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Current Opinion in Genetics & Development 35 (2015): 66-72, doi:10.1016/j.gde.2015.10.003.Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world.S.M.G. was supported by an EPA STAR Graduate Fellowship and by NIH training grant 5T-32EB-009412.2016-11-1

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota.

Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn\u27s disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort of metagenomes from 186 people, including a metabolically healthy population and individuals with type 1 and type 2 diabetes. Model results showed that individual bacterial genera maintained conserved niche structures across humans, while the community-level production of short-chain fatty acids (SCFAs) was heterogeneous and highly individual specific. Model output revealed complex cross-feeding interactions that would be difficult to measur

Analisis Faktor yang Mempengaruhi Pendapatan USAhatani Sayuran di Kecamatan Sungai Gelam Kabupaten Muaro Jambi

Penelitian ini bertujuan untuk melihat besarnya pendapatan USAhatani sayuran di Kecamatan Sungai Gelam Kabupaten Muaro Jambi. Pemilihan lokasi penelitian dilakukan dengan sengaja atas dasar pertimbangan bahwa di Kecamatan Sungai Gelam merupakan salah satu daerah yang mengusahakan sayuran terbesar di Kabupaten Muaro Jambi.Sampel dalam penelitian ini adalah petani sayuran di Kecamatan Sungai Gelam Kabupaten Muaro Jambi.Penelitian dilakukan dari tanggal 10 September 2014 sampai dengan tanggal 10 Oktober 2014 dengan menggunakan metode simple random sampling. Hasil penelitian ini menunjukkan bahwa Rata – rata pendapatan USAhatani sayuran petani responden di daerah penelitian yaitu Rp. 21.673.293,87 /Tahun dengan rata – rata luas lahan sebesar 0,26 ha. Data ini menunjukkan bahwa kegiatan USAhatani sayuran yang dilakukan petani di Kecamatan Sungai Gelam Masih berskala kecil.Pendapatan USAhatani sayuran di daerah penelitian secara nyata dipengaruhi oleh variabel luas lahan dan modal dengan nilai koefisien positif.Hal ini berarti semakin tinggi luas lahan dan modal yang digunakan, maka pendapatan USAhatani sayuran tinggi.Sedangkan tenaga kerja tidak memberikan pengaruh secara nyata terhadap pendapatan USAhatani sayuran

Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities.

Background: Changes in aboveground community composition and diversity following shrub encroachment have been studied extensively. Recently, shrub encroachment was associated with differences in belowground bacterial communities relative to non-encroached grassland sites hundreds of meters away. This spatial distance between grassland and shrub sites left open the question of how soil bacterial communities associated with different vegetation types might differ within the same plot location. Methods: We examined soil bacterial communities between shrub-encroached and adjacent (one m apart) grassland soils in Chinese Inner Mongolian, using high-throughput sequencing method (Illumina, San Diego, CA, USA). Results: Shrub-encroached sites were associated with dramatic restructuring of soil bacterial community composition and predicted metabolic function, with significant increase in bacterial alpha-diversity. Moreover, bacterial phylogenic structures showed clustering in both shrub-encroached and grassland soils, suggesting that each vegetation type was associated with a unique and defined bacterial community by niche filtering. Finally, soil organic carbon (SOC) was the primary driver varied with shifts in soil bacterial community composition. The encroachment was associated with elevated SOC, suggesting that shrub-mediated shifts in SOC might be responsible for changes in belowground bacterial community. Discussion: This study demonstrated that shrub-encroached soils were associated with dramatic restructuring of bacterial communities, suggesting that belowground bacterial communities appear to be sensitive indicators of vegetation type. Our study indicates that the increased shrub-encroached intensity in Inner Mongolia will likely trigger large-scale disruptions in both aboveground plant and belowground bacterial communities across the region