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"Microbial ecology"

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https://www.readbyqxmd.com/read/28934589/low-dietary-protein-and-high-carbohydrate-infant-formula-affects-the-microbial-ecology-of-the-large-intestine-in-neonatal-rats
#1
Wenguang Fan, Haiwei Ren, Yingying Cao, Yonggang Wang, Guicheng Huo
The aim of this study was to investigate the effects of a low dietary protein and high carbohydrate infant formula on the large intestine of neonatal rats. A total of 24 neonatal SD rats (14d old) were randomly assigned to the low-protein, high-carbohydrate infant formula-fed group (IF group) and a human breast milk-fed group (HF group). After 7 days, we selected 6 rats at random from each group to study. No significantly different microbial colonization patterns were observed in the two groups at the phylum level...
September 21, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28929212/an-insight-into-phage-diversity-at-environmental-habitats-using-comparative-metagenomics-approach
#2
Krupa Parmar, Nishant Dafale, Rajesh Pal, Hitesh Tikariha, Hemant Purohit
Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses...
September 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28928718/analysing-microbial-community-composition-through-amplicon-sequencing-from-sampling-to-hypothesis-testing
#3
REVIEW
Luisa W Hugerth, Anders F Andersson
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28916990/transformation-of-anaerobic-granules-into-aerobic-granules-and-the-succession-of-bacterial-community
#4
Haohao Sun, Ping Yu, Qiaoling Li, Hongqiang Ren, Bo Liu, Lin Ye, Xu-Xiang Zhang
In this study, we demonstrated that anaerobic granular sludge could be successfully transformed into aerobic granular sludge in a continuous up-flow reactor in 45 days. An aerobic microbial community successfully developed in the granules and high organic matter and nitrogen removal performance was achieved. Under an ammonia nitrogen loading rate of 0.8 kg N/(m(3) day), ammonia nitrogen and the total nitrogen removal efficiency of the reactor reached up to 100 and 93%, respectively. An obvious bacterial community shift in granular sludge was observed during the transformation process...
September 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28904415/targeted-metagenome-based-analyses-show-gut-microbial-diversity-of-inflammatory-bowel-disease-patients
#5
Zhibing Qiu, Haijing Yang, Lan Rong, Weiqun Ding, Jiazhen Chen, Liang Zhong
Inflammatory bowel disease (IBD) is a multifactorial disease including both genetic and environmental factors. We compared the diversity of intestinal microbesamong a cohort of IBD patients to study the microbial ecological effects on IBD. Fecal samples from patients were sequenced with next generation sequence technology at 16S rDNA region. With statistical tools, microbial community was investigated at different level. The gut microbial diversity of Crohn's disease (CD) patients and colonic polyp (CP) patients significantly different from each other...
September 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28904265/changes-in-gut-microbial-ecology-and-immunological-responses-of-mice-fed-the-insoluble-fraction-of-brassica-rapa-l-that-was-fermented-or-not
#6
Sachi Tanaka, Kana Yamamoto, Chisato Hamajima, Fuka Takahashi, Kazuki Yamada, Kanon Furuya, Yutaka Uyeno
We aimed to investigate the effects of feeding fermented Brassica rapa L. on ecological and immunological changes in the mouse gut using in vitro cultivation tests and in vivo experiments in normal mice. In the preliminary in vitro study, two B. rapa L. products from different fermentation periods (one d [SF] or six months [LF]) were evaluated along with non-fermented vegetables (NF). Among the components of each product, the insoluble fraction resulted in the most prominent change such as a relative increase in butyrate production during a cultivation inoculated with mouse cecum contents...
September 12, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28894651/metacrast-reference-guided-extraction-of-crispr-spacers-from-unassembled-metagenomes
#7
Abraham G Moller, Chun Liang
Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool-MetaCRAST) that constrains searches based on user-specified direct repeats (DRs)...
2017: PeerJ
https://www.readbyqxmd.com/read/28884952/soluble-dietary-fiber-reduces-trimethylamine-metabolism-via-gut-microbiota-and-co-regulates-host-ampk-pathways
#8
Qian Li, Tao Wu, Rui Liu, Min Zhang, Ruijun Wang
SCOPE: Evidence from animal experiments and clinical medicine suggest that high dietary fiber intake, followed by gut microbiota-mediated fermentation, decreases trimethylamine (TMA) metabolism, the mechanism of which, however, remains unclear. The objective of this analysis was to evaluate, using mice fed with red meat, the effects of soluble dietary fiber (SDF) intervention on TMA metabolism. METHODS AND RESULTS: Low- or high-dose soluble dietary fiber (SDF) from natural wheat bran (LN and HN, low- and high-dose natural SDF), fermented wheat bran (LF and HF, low- and high-dose fermented SDF), and steam-exploded wheat bran (LE and HE, low- and high-dose exploded SDF groups) were used to examine whether SDF interventions in mice fed with red meat can alter TMA and trimethylamine N-oxide (TMAO) metabolism by gut microbial communities in a diet-specific manner...
September 8, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28883811/culture-media-and-individual-hosts-affect-the-recovery-of-culturable-bacterial-diversity-from-amphibian-skin
#9
Daniel Medina, Jenifer B Walke, Zachary Gajewski, Matthew H Becker, Meredith C Swartwout, Lisa K Belden
One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28878747/in-vitro-antibacterial-activity-of-unconjugated-and-conjugated-bile-salts-on-staphylococcus-aureus
#10
Thippeswamy H Sannasiddappa, Peter A Lund, Simon R Clarke
Bile salts are potent antimicrobial agents and are an important component of innate defenses in the intestine, giving protection against invasive organisms. They play an important role in determining microbial ecology of the intestine and alterations in their levels can lead to increased colonization by pathogens. We have previously demonstrated survival of the opportunistic pathogen Staphylococcus aureus in the human colonic model. Thus investigating the interaction between S. aureus and bile salts is an important factor in understanding its ability to colonize in the host intestine...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28878171/lactobacillus-sakei-a-starter-for-sausage-fermentation-a-protective-culture-for-meat-products
#11
REVIEW
Monique Zagorec, Marie-Christine Champomier-Vergès
Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture...
September 6, 2017: Microorganisms
https://www.readbyqxmd.com/read/28865967/bugging-allergy-role-of-pre-pro-and-synbiotics-in-allergy-prevention
#12
REVIEW
Christina E West, Majda Dzidic, Susan L Prescott, Maria C Jenmalm
Large-scale biodiversity loss and complex changes in social behaviors are altering human microbial ecology. This is increasingly implicated in the global rise in inflammatory diseases, most notably the "allergy epidemic" in very early life. Colonization of human ecological niches, particularly the gastrointestinal tract, is critical for normal local and systemic immune development and regulation. Disturbances in composition, diversity and timing of microbial colonization have been associated with increased allergy risk, indicating the importance of strategies to restore a dysbiotic gut microbiota in the primary prevention of allergic diseases, including the administration of probiotics, prebiotics and synbiotics...
August 30, 2017: Allergology International: Official Journal of the Japanese Society of Allergology
https://www.readbyqxmd.com/read/28856796/environmental-niches-and-metabolic-diversity-in-neoarchean-lakes
#13
E E Stüeken, R Buick, R E Anderson, J A Baross, N J Planavsky, T W Lyons
The diversification of macro-organisms over the last 500 million years often coincided with the development of new environmental niches. Microbial diversification over the last 4 billion years likely followed similar patterns. However, linkages between environmental settings and microbial ecology have so far not been described from the ancient rock record. In this study, we investigated carbon, nitrogen, and molybdenum isotopes, and iron speciation in five non-marine stratigraphic units of the Neoarchean Fortescue Group, Western Australia, that are similar in age (2...
August 30, 2017: Geobiology
https://www.readbyqxmd.com/read/28854287/risk-of-superinfection-in-peri-implantitis-after-systemic-broad-spectrum-antibiotics
#14
Fernando Verdugo
Peri-implant disease has developed over the last few years as a complication that is often difficult to resolve. The disease process is mainly attributed to bacterial infection. Proposed combined therapies use broad-spectrum antibiotics to halt its progression. A major associated risk is the undetected development of superinfections that are difficult to eradicate. A group of healthy individuals with advanced peri-implantitis (PI) were referred for evaluation due to severe, rapidly progressive bone loss. Previous nonsurgical and empiric antibiotic therapy had been rendered...
August 30, 2017: International Journal of Periodontics & Restorative Dentistry
https://www.readbyqxmd.com/read/28851370/comparing-microbiota-profiles-in-induced-and-spontaneous-sputum-samples-in-copd-patients
#15
Solveig Tangedal, Marianne Aanerud, Rune Grønseth, Christine Drengenes, Harald G Wiker, Per S Bakke, Tomas M Eagan
BACKGROUND: Induced and spontaneous sputum are used to evaluate the airways microbiota. Whether the sputum types can be used interchangeably in microbiota research is unknown. Our aim was to compare microbiota in induced and spontaneous sputum from COPD patients sampled during the same consultation. METHODS: COPD patients from Bergen, Norway, were followed between 2006/2010, examined during the stable state and exacerbations. 30 patients delivered 36 sample pairs...
August 29, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28844839/microbial-dynamics-in-petroleum-oilfields-and-their-relationship-with-physiological-properties-of-petroleum-oil-reservoirs
#16
REVIEW
Sunita J Varjani, Edgard Gnansounou
Petroleum is produced by thermal decay of buried organic material over millions of years. Petroleum oilfield ecosystems represent resource of reduced carbon which favours microbial growth. Therefore, it is obvious that many microorganisms have adapted to harsh environmental conditions of these ecosystems specifically temperature, oxygen availability and pressure. Knowledge of microorganisms present in ecosystems of petroleum oil reservoirs; their physiological and biological properties help in successful exploration of petroleum...
August 9, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28843369/microbial-ecology-of-cereal-vinegar-fermentation-insights-for-driving-the-ecosystem-function
#17
REVIEW
Zhen-Ming Lu, Zong-Min Wang, Xiao-Juan Zhang, Jian Mao, Jin-Song Shi, Zheng-Hong Xu
Over thousands of years, humans have mastered the natural vinegar fermentation technique of cultivating functional microbiota on different raw materials. Functional microbial communities that form reproducibly on non-autoclaved raw materials through repeated batch acetic acid fermentation underpin the flavour development of traditional cereal vinegars. However, how to modulate rationally and optimise the metabolic function of these naturally engineered acidic ecosystems remains unclear. Exploring two key minorities in a vinegar ecosystem, including microbial functions (e...
August 24, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28831604/distinct-taxonomic-and-functional-composition-of-soil-microbiomes-along-the-gradient-forest-restinga-mangrove-in-southeastern-brazil
#18
Lucas William Mendes, Siu Mui Tsai
Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters...
August 22, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28827029/temporal-assessment-of-microbial-communities-in-soils-of-two-contrasting-mangroves
#19
Janaina Rigonato, Angela D Kent, Thiago Gumiere, Luiz Henrique Zanini Branco, Fernando Dini Andreote, Marli Fátima Fiore
Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotrophs) fingerprinting. The data presented herein indicated that changes in all the communities evaluated were mainly driven by the temporal effect in the contaminated area, while local effects were dominant on the pristine mangrove...
August 1, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28826938/development-of-the-gut-microbiota-in-infancy-and-its-impact-on-health-in-later-life
#20
REVIEW
Masaru Tanaka, Jiro Nakayama
Gut microbial ecology and function are dynamic in infancy, but are stabilized in childhood. The 'new friends' have a great impact on the development of the digestive tract and host immune system. In the first year of life, especially, the gut microbiota dramatically changes through interactions with the developing immune system in the gut. The process of establishing the gut microbiota is affected by various environmental factors, with the potential to be a main determinant of life-long health. In this review, we summarize recent findings regarding gut microbiota establishment, including the importance of various factors related to the development of the immune system and allergic diseases later in life...
August 17, 2017: Allergology International: Official Journal of the Japanese Society of Allergology
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