Microbial Isolation

The importance of isolating a microbe from the environment, such as food (solid substrate), drinks (liquid substrate), and yourself because of the many microbes that are difficult to observe or distinguish directly using the five senses. A sample can contain bacteria or fungi. By isolating, the shape of the colonies and the contents in a sample can be observed. Bacteria from the air and normal flora form colonies with lobate-shaped edges, whereas bacteria found in well water samples form colonies with irregular edges and there are also fungi found in the well water samples

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.- Background - Results -- Authentication of a preserved oral biofilm in calculus samples -- Dental calculus and plaque biofilm communities are distinct -- Health-associated communities of dental plaque and calculus are distinct -- Signatures of health and of disease are shared in modern and historic calculus samples -- Microbial community differences between health and disease in calculus are poorly resolved -- Absence of caries-specific microbial profiles in dental calculus -- Microbial co-exclusion patterns in plaque and calculus reflect biofilm maturity -- Microbial complexes in plaque and calculus -- Functional prediction in calculus is poorly predictive of health status -- Proteomic profiles of historic healthy site calculus -- Correlations between taxonomic, proteomic, and metabolomic profiles - Discussion - Conclusions - Materials and methods --Historic and modern calculus sample collection DNA extraction -- DNA library construction and high-throughput sequencing -- DNA sequence processing -- Genetic assessment of historic calculus sample preservation -- Genetic microbial taxonomic profiling -- Principal component analysis -- Assessment of differentially abundant taxa -- Sparse partial least squares-discriminant analysis -- Assessment of microbial co-exclusion patterns -- Gene functional categorization with SEED -- Proteomics -- Metabolomics -- Regularized canonical correlation analysi

Assessment of tillage systems in organic farming: influence of soil structure on microbial biomass. First results

Soil tillage modifies environmental conditions of soil microorganisms and their ability to release nitrogen. We compare the influence of reduced tillage (RT) and mouldboard ploughing (MP) on the soil microbial functioning in organic farming. In order to connect soil structure generated by these tillage systems on the soil microbial biomass we adopt a particular sampling scheme based on the morphological characterisation of the soil structure by the description of the soil profile. This method reveals the influence of soil structure on soil microbial biomass and allows a more precise assessment of the impact of tillage managements on the soil microbial functioning

Microbial community pattern detection in human body habitats via ensemble clustering framework

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural patterns. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.Comment: BMC Systems Biology 201

Citric Acid and Microbial Phytase Inclusion in the Diet to Improve Utilization Phytate Phosporus and Growth of Broiler

Penelitian ini menggunakan anak ayam umur 3 sampai dengan 38 hari (180 ekor) dan 7 sampai dengan 42 hari (180 ekor). Ayam diberi ransum A, B, dan C yang berbahan dasar jagung (CSM) dan ransum E, F, dan G yang berbahan dasar gandum (WSM) yang diberi perlakuan penambahan steam pada suhu 1000C selama 10 menit. Semua ransum ditambah enzim fitase (SP-1002 ct) sebanyak 500 U/kg dan dibuat dalam bentuk pelet. Khusus ransum C dan G ditambah asam sitrat. Kandungan fosfor total ransum adalah 4,5 g/kg dan fosfor tersedia adalah 1,5 g/kg (defisien P). Bobot badan harian adalah 36, 34, dan 45 g/hari untuk ayam yang diberi ransum A, B, dan C dan 54, 46, dan 55 g/hari untuk ransum E, F, dan G. Deposisi fosfor total adalah 5,75; 5,36; dan 6,99 g berturut-turut untuk ransum A, B dan C dan 8,15; 6,90; dan 7,77 g untuk E, F, dan G. Penambahan asam sitrat dalam ransum CSM yang mengandung enzim fitase rendah mampu meningkatkan pertumbuhan dan deposisi fosfor. Pada ransum WSM, perlakuan panas menyebabkan penurunan aktifitas fitase dan penurunan ini tidak dapat digantikan dengan penambahan enzim fitase (microbial phytase) akan tetapi dapat digantikan dengan penambahan asam sitrat. Hasil penelitian ini dapat disimpulkan bahwa asam sitrat berpengaruh terhadap efisiensi enzim fitase (microbial phytase) dalam mendegradasi senyawa fitat di dalam saluran pencernaan

Synthetic microbial ecosystems : an exciting tool to understand and apply microbial communities

Many microbial ecologists have described the composition of microbial communities in a plenitude of environments, which has greatly improved our basic understanding of microorganisms and ecosystems. However, the factors and processes that influence the behaviour and functionality of an ecosystem largely remain black boxes when using conventional approaches. Therefore, synthetic microbial ecology has gained a lot of interest in the last few years. Because of their reduced complexity and increased controllability, synthetic communities are often preferred over complex communities to examine ecological theories. They limit the factors that influence the microbial community to a minimum, allowing their management and identifying specific community responses. However, besides their use for basic research, synthetic ecosystems also found their way towards different applications, like industrial fermentation and bioremediation. Here, we review why and how synthetic microbial communities are applied for research purposes and for which applications they have been and could be successfully used

Grazing impact on soil chemical and biological properties under different plant cover types in a mountain area of Southern Italy.

Grazing can contribute to soil degradation by compaction due to roaming of livestock and loss of herbaceous cover, affecting also soil microbial community. Aim of this study was to assess grazing impact on soil microbial community and nutrient status under different plant cover types (i.e., fernery, chestnut wood, garigue). Grazed and ungrazed soils were analysed for water holding capacity, pH, organic carbon, N, S, K, Mg, Fe, Mn, Zn and Cu content, microbial biomass, fungal mycelium and potential respiration. Moreover, some ecophysiological indices, as microbial quotient, coefficient of endogenous mineralization (CEM), metabolic quotient (qCO2) and fungal fraction of microbial carbon were calculated. The results of present study showed that a moderate intensity grazing had low or no impact on chemical characteristics of soils and affects microbial community mainly in grazed areas with lower vegetation cover and lower content of nutrient and organic carbon, compared to areas with a thick layer of vegetation

A new model for the formation of microbial polygons in a coastal sabkha setting

The stratigraphic record of microbially induced sedimentary structures spans most of the depositional record. Today, microbes continue to generate, bind and modify sediments in a vast range of depositional environments. One of the most cited of these settings is the coastal microbial mat system of the Persian/Arabian Gulf. In this setting, an extensive zone of microbial mat polygons has previously been interpreted as resulting from desiccation‐related contraction during episodic drying. This study employs 15 years of field‐based monitoring of the interaction between environmental factors and the development and evolution of polygon morphologies to test the desiccation model in this setting. On the basis of these observations, a new model is proposed that accounts for the genesis and development of microbial polygons without the need for desiccation‐induced shrinkage. Conversely, the formation, development and erosion of microbial polygons is a direct result of the production of large amounts of organic matter in a healthy, yet spatially limited, microbial community. The recognition of microbial polygons has previously been applied as a diagnostic tool for the reconstruction of ancient depositional environments. The present study calls these interpretations into doubt. It is inferred that preservation of the microbial polygons as a recognizable form would be rare. Biological degradation and compaction will reduce polygons to produce the ‘wispy’ laminae that are a common feature of ancient sabkha lithofacies

A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities

A fundamental goal in microbiome studies is determining which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative, rather than absolute abundances. Moreover, studies often analyze only stool, despite microbial diversity differing substantially among gastrointestinal (GI) locations. Here, we develop a quantitative framework to measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compare microbial loads in lumenal and mucosal samples along the GI tract. Quantitative measurements of absolute (but not relative) abundances reveal decreases in total microbial loads on the ketogenic diet and enable us to determine the differential effects of diet on each taxon in stool and small-intestine mucosa samples. This rigorous quantitative microbial analysis framework, appropriate for diverse GI locations enables mapping microbial biogeography of the mammalian GI tract and more accurate analyses of changes in microbial taxa in microbiome studies