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Title: PyNAST: a flexible tool for aligning sequences to a template alignment

Journal Article · · Bioinformatics
 [1];  [2];  [2];  [3];  [3];  [4]
  1. Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry; DOE/OSTI
  2. Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Microbiology
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Center for Environmental Biotechnology
  4. Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry
+ Show Author Affiliations

Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API). Results: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis. Availability: PyNAST is available at http://pynast.sourceforge.net.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625264
Journal Information:
Bioinformatics, Journal Name: Bioinformatics Journal Issue: 2 Vol. 26; ISSN 1367-4803
Publisher:
International Society for Computational Biology - Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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  • Kreisinger, Jakub; Bastien, Géraldine; Hauffe, Heidi C.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, Issue 1675 https://doi.org/10.1098/rstb.2014.0295
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Dietary shifts influenced by livestock grazing shape the gut microbiota composition and co-occurrence networks in a local rodent species journal November 2018
In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field: Differences in deep-sea hydrothermal fluid samples journal November 2012
Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors: Microbiota in oesophageal diseases and PPI therapy journal October 2013
Herbivorous rodents ( N eotoma spp. ) harbour abundant and active foregut microbiota: Foregut microbes in herbivorous woodrats journal January 2014
The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey: Microbial community of syntrophic enrichment cultures journal October 2014
Microbial cargo: do bacteria on symbiotic propagules reinforce the microbiome of lichens?: Bacterial cargo on lichen propagules journal December 2014
Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems: Diversity and biogeography of benthic microeukaryotes journal February 2015
Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets: Tannin-degrading bacteria aid hosts consuming tannins journal April 2015
Physicochemical control of bacterial and protist community composition and diversity in Antarctic sea ice: Physicochemical control of sea ice microbial communities journal May 2015
Environmental filtering decreases with fish development for the assembly of gut microbiota: Gut microbiota assembly across fish development journal June 2016
Field‐based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils journal July 2016
Methanogenic paraffin degradation proceeds via alkane addition to fumarate by ‘Smithella’ spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens : Methanogenic paraffin-utilizing consortium journal June 2016
Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences: Swine mucosa-associated gut microbiota journal January 2017
Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean: Iceberg influence on bacterioplankton journal May 2017
Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective journal June 2017
Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition journal July 2017
Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities: Dispersal structures sediment microbial communities journal February 2018
High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity: Moss and litter-associated protists journal March 2018
Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval , , journal March 2015
Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm journal October 2013
Characterizing changes in soil bacterial community structure in response to short-term warming journal February 2014
Effects of light and prey availability on Arctic freshwater protist communities examined by high-throughput DNA and RNA sequencing journal April 2014
Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts journal November 2014
Diversity and dynamics of microbial communities in brown planthopper at different developmental stages revealed by high‐throughput amplicon sequencing journal November 2019
Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics journal October 2013
Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure journal July 2015
Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows journal February 2016
Different response of bacteria, archaea and fungi to process parameters in nine full‐scale anaerobic digesters journal April 2019
Air‐side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome journal July 2019
Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data journal October 2013
Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome journal May 2018
Gut microbiome in children with enthesitis-related arthritis in a developing country and the effect of probiotic administration journal December 2016
Determinism of bacterial metacommunity dynamics in the southern East China Sea varies depending on hydrography journal July 2014
Microbial biogeography of permafrost thaw ponds across the changing northern landscape journal August 2015
Feedstock determines biochar-induced soil priming effects by stimulating the activity of specific microorganisms: Feedstock of biochar determines priming effects journal February 2018
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding journal August 2013
Microbial ecosystems are dominated by specialist taxa journal August 2015
Biochar alters the soil microbiome and soil function: results of next-generation amplicon sequencing across Europe journal July 2016
Local and geographical factors jointly drive elevational patterns in three microbial groups across subarctic ponds: TEITTINEN et al. journal June 2017
Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from Kenya journal September 2012
Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes: Bacterial biogeography in arctic soils journal November 2010
The intestinal microbiota in aged mice is modulated by dietary resistant starch and correlated with improvements in host responses journal September 2012
Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout journal March 2018
Insect exclusion limits variation in bacterial microbiomes of tomato flowers and fruit journal October 2018
Autochthonous probiotic bacteria modulate intestinal microbiota of Pirarucu, Arapaima gigas journal July 2019
Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska journal December 2014
Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts journal June 2015
Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee journal April 2016
Metabarcoding reveals environmental factors influencing spatio‐temporal variation in pelagic micro‐eukaryotes journal July 2016
Microbiome changes through ontogeny of a tick pathogen vector journal September 2016
Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China) journal May 2017
Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring journal September 2017
Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract journal December 2017
Influence of immunogenetics, sex and body condition on the cutaneous microbial communities of two giant salamanders journal March 2018
Alternate life history phases of a common seaweed have distinct microbial surface communities journal August 2018
Dietary specialization in mutualistic acacia-ants affects relative abundance but not identity of host-associated bacteria journal August 2018
Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower ( Mimulus guttatus ) floral microbiome journal November 2019
Impact of dietary induced precocious gut maturation on cecal microbiota and its relation to the blood-brain barrier during the postnatal period in rats journal January 2018
Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island journal October 2017
Fragile skin microbiomes in megacities are assembled by a predominantly niche-based process journal March 2018
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice journal September 2013
Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation journal July 2014
Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy journal November 2015
Natural polyreactive IgA antibodies coat the intestinal microbiota journal September 2017
The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients journal January 2018
Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice journal March 2017
Bacterial colonization and succession in a newly opened hospital journal May 2017
Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells journal November 2018
Molecular Microbiological Profile of Chronic Suppurative Otitis Media journal October 2016
New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea journal May 2019
A Long-Standing Complex Tropical Dipole Shapes Marine Microbial Biogeography journal September 2018
Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada journal August 2016
Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants journal September 2013
Reduced-Particle-Size Wheat Bran Is Efficiently Colonized by a Lactic Acid-Producing Community and Reduces Levels of Enterobacteriaceae in the Cecal Microbiota of Broilers journal November 2018
Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients journal November 2016
Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline journal November 2017
Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota journal July 2014
“Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese journal August 2012
Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics journal August 2014
From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation journal November 2015
Cell Size Distributions of Soil Bacterial and Archaeal Taxa journal September 2013
A Hidden Pitfall in the Preparation of Agar Media Undermines Microorganism Cultivability journal October 2014
Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert journal March 2014
Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms journal March 2017
Biogeography of the Sediment Bacterial Community Responds to a Nitrogen Pollution Gradient in the East China Sea journal March 2014
Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States journal July 2011
Validating DNA Extraction Protocols for Bentonite Clay journal October 2019
The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations journal July 2015
Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption journal May 2015
The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility journal August 2016
Altered Oral Viral Ecology in Association with Periodontal Disease journal July 2014
Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients journal July 2019
Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity journal March 2018
Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in Drosophila melanogaster journal November 2017
Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development journal May 2018
pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures journal May 2017
Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information journal August 2017
Fecal Components Modulate Human Astrovirus Infectivity in Cells and Reconstituted Intestinal Tissues journal December 2019
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation journal December 2015
Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem journal March 2017
Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes journal September 2019
Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention journal July 2017
AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition journal July 2013
A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota journal September 2017
The human milk oligosaccharide 2′-fucosyllactose augments the adaptive response to extensive intestinal journal March 2016
Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle journal January 2013
Structural changes in the gut microbiome of constipated patients journal September 2014
Toxoplasma gondii- Induced Long-Term Changes in the Upper Intestinal Microflora during the Chronic Stage of Infection journal November 2018
Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH journal January 2018
Blueberry Attenuates Liver Fibrosis, Protects Intestinal Epithelial Barrier, and Maintains Gut Microbiota Homeostasis journal November 2019
Microbial Community Changes in the Rhizosphere Soil of Healthy and Rusty Panax ginseng and Discovery of Pivotal Fungal Genera Associated with Rusty Roots journal January 2020
Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm
  • Pampillón-González, Liliana; Ortiz-Cornejo, Nadia L.; Luna-Guido, Marco
  • Journal of Molecular Microbiology and Biotechnology, Vol. 27, Issue 5 https://doi.org/10.1159/000479108
journal January 2017
The Role of Bacteria in the Pathogenesis and Progression of Idiopathic Pulmonary Fibrosis journal October 2014
Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12 journal February 2018
The bacterial composition of ventilation filter dust in Norwegian pre-school nurseries journal June 2017
Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation journal July 2013
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life journal January 2013
Community differentiation of the cutaneous microbiota in psoriasis journal December 2013
Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis journal January 2014
Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation journal December 2016
Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli journal June 2020
The gut microbiota of Colombians differs from that of Americans, Europeans and Asians journal December 2014
High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia journal January 2015
Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses journal January 2017
Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage journal March 2017
Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle journal April 2017
Comparison of rumen bacterial communities in dairy herds of different production journal August 2017
Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis journal August 2018
Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study journal December 2018
How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies journal July 2020
Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration journal November 2017
Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients journal August 2017
Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing journal October 2014
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity journal November 2019
Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria journal February 2016
Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system journal June 2016
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants journal July 2016
Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis journal November 2014
Thermal discharge-created increasing temperatures alter the bacterioplankton composition and functional redundancy journal September 2016
Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults journal June 2018
Metagenomic analysis and the functional profiles of traditional fermented pork fat ‘sa-um’ of Northeast India journal October 2018
The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites journal January 2015
Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants journal April 2015
An accurate and efficient experimental approach for characterization of the complex oral microbiota journal October 2015
Phylogenetic approaches to microbial community classification journal October 2015
Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences journal December 2015
Microbial biogeography of a university campus journal December 2015
Diet may influence the oral microbiome composition in cats journal June 2016
Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns journal October 2016
Host genetic variation in mucosal immunity pathways influences the upper airway microbiome journal February 2017
New evidences on the altered gut microbiota in autism spectrum disorders journal February 2017
Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome journal August 2017
Individual signatures and environmental factors shape skin microbiota in healthy dogs journal October 2017
Indoor microbiota in severely moisture damaged homes and the impact of interventions journal October 2017
Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment journal November 2017
Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis journal January 2018
Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control journal February 2018
Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization journal September 2018
Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure journal October 2018
Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR journal May 2019
A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals journal May 2020
Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata journal June 2020
Fetal exposure to maternal inflammation interrupts murine intestinal development and increases susceptibility to neonatal intestinal injury journal January 2019
A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable journal November 2012
Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States journal January 2013
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments journal February 2013
The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations journal February 2013
Control of Temperature on Microbial Community Structure in Hot Springs of the Tibetan Plateau journal May 2013
Season, Irrigation, Leaf Age, and Escherichia coli Inoculation Influence the Bacterial Diversity in the Lettuce Phyllosphere journal July 2013
Comprehensive Genomic Characterization of Campylobacter Genus Reveals Some Underlying Mechanisms for its Genomic Diversification journal August 2013
Development of the Preterm Gut Microbiome in Twins at Risk of Necrotising Enterocolitis and Sepsis journal August 2013
Bacterial Community Mapping of the Mouse Gastrointestinal Tract journal October 2013
A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees journal October 2013
Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil journal October 2013
A Cross-Sectional Survey of Bacterial Species in Plaque from Client Owned Dogs with Healthy Gingiva, Gingivitis or Mild Periodontitis journal December 2013
The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease journal January 2014
Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments journal July 2014
Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing journal August 2014
Bacterial Endophytic Communities in the Grapevine Depend on Pest Management journal November 2014
Cultivation-Based and Molecular Assessment of Bacterial Diversity in the Rhizosheath of Wheat under Different Crop Rotations journal June 2015
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities journal June 2015
Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus journal October 2015
Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study journal October 2015
The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations journal October 2015
Functional Metagenomics of the Bronchial Microbiome in COPD journal December 2015
Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice journal January 2016
Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study journal April 2016
Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions journal May 2016
Seasonality and Locality Affect the Diversity of Anopheles gambiae and Anopheles coluzzii Midgut Microbiota from Ghana journal June 2016
Using a Control to Better Understand Phyllosphere Microbiota journal September 2016
The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health journal October 2016
Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine journal January 2017
Olive oil bioactives protect pigs against experimentally-induced chronic inflammation independently of alterations in gut microbiota journal March 2017
Microbiomes associated with infective stages of root-knot and lesion nematodes in soil journal May 2017
Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing journal May 2017
The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats journal June 2017
Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’ journal March 2018
Diversity and antimicrobial potential in sea anemone and holothurian microbiomes journal May 2018
Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis journal October 2018
Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi journal December 2018
Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure journal April 2019
Gut microbiota profiling in Norwegian weaner pigs reveals potentially beneficial effects of a high-fiber rapeseed diet journal December 2018
An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments journal March 2019
[NiFe]-hydrogenases are constitutively expressed in an enriched Methanobacterium sp. population during electromethanogenesis journal April 2019
Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination journal June 2019
Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets journal July 2019
OGG1 deficiency alters the intestinal microbiome and increases intestinal inflammation in a mouse model journal January 2020
The composition of the gut microbiota shapes the colon mucus barrier journal December 2014
Responsiveness of cardiometabolic-related microbiota to diet is influenced by host genetics text January 2014
Temporal dynamics in the ruminal microbiome of dairy cows during the transition period journal September 2014
Dynamics of Vaginal and Rectal Microbiota Over Several Menstrual Cycles in Female Cynomolgus Macaques journal June 2019
Soil Salinity Controls Relative Abundance of Specific Bacterial Groups Involved in the Decomposition of Maize Plant Residues journal May 2018
Estimating the Intra-taxa Diversity, Population Genetic Structure, and Evolutionary Pathways of Cryptococcus neoformans and Cryptococcus gattii journal April 2018
Oral Administration of Compound Probiotics Improved Canine Feed Intake, Weight Gain, Immunity and Intestinal Microbiota journal April 2019
Seasonal and Interannual Changes in Ciliate and Dinoflagellate Species Assemblages in the Arctic Ocean (Amundsen Gulf, Beaufort Sea, Canada) journal February 2017
Two distinct microbial communities revealed in the sponge Cinachyrella journal November 2014
Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism journal January 2015
The human urine virome in association with urinary tract infections journal January 2015
Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils journal February 2015
Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania journal March 2015
Insights into the bacterial community and its temporal succession during the fermentation of wine grapes journal August 2015
Rumen microbial communities influence metabolic phenotypes in lambs journal October 2015
The effect of diet and host genotype on ceca microbiota of Japanese quail fed a cholesterol enriched diet journal October 2015
Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues journal October 2015
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing journal October 2015
Comparative Gut Microbiota of 59 Neotropical Bird Species journal December 2015
High-Up: A Remote Reservoir of Microbial Extremophiles in Central Andean Wetlands journal December 2015
A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities journal January 2016
Human Microbiota of the Argentine Population- A Pilot Study journal February 2016
Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology journal April 2016
Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves journal May 2016
Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities journal May 2016
Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium journal May 2016
Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data journal May 2016
The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health journal November 2016
Nutritional Models of Experimentally-Induced Subacute Ruminal Acidosis (SARA) Differ in Their Impact on Rumen and Hindgut Bacterial Communities in Dairy Cows journal January 2017
Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird journal February 2017
Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome journal May 2017
Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters journal June 2017
Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs journal July 2017
Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) journal July 2017
Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy journal October 2017
Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei journal December 2017
Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies journal February 2018
Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification journal February 2018
Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny journal March 2018
Gut Microbiota Profiling and Gut–Brain Crosstalk in Children Affected by Pediatric Acute-Onset Neuropsychiatric Syndrome and Pediatric Autoimmune Neuropsychiatric Disorders Associated With Streptococcal Infections journal April 2018
Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers journal May 2018
Microscale Biosignatures and Abiotic Mineral Authigenesis in Little Hot Creek, California journal May 2018
Effectiveness of Interventions to Modulate the Rumen Microbiota Composition and Function in Pre-ruminant and Ruminant Lambs journal June 2018
Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community journal June 2018
Low-Temperature Sulfidic-Ice Microbial Communities, Borup Fiord Pass, Canadian High Arctic journal July 2018
Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility journal October 2018
Dynamic Distribution of Gut Microbiota in Goats at Different Ages and Health States journal October 2018
Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions journal November 2018
The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities journal July 2019
Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species journal September 2019
Serotonin Transporter Genotype Modulates the Gut Microbiota Composition in Young Rats, an Effect Augmented by Early Life Stress journal August 2017
Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang journal September 2016
The Effects of Feeding a Soybean-Based or a Soy-Free Diet on the Gut Microbiome of Pasture-Raised Chickens Throughout Their Lifecycle journal May 2019
Effects of Nanoparticles on Plant Growth-Promoting Bacteria in Indian Agricultural Soil journal March 2019
Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations journal May 2019
Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism? journal February 2018
Descriptive Bacterial and Fungal Characterization of Propolis Using Ultra-High-Throughput Marker Gene Sequencing journal November 2019
Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota journal June 2018
Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source journal August 2018
Diversity of Gut Microbiota Affecting Serum Level of Undercarboxylated Osteocalcin in Patients with Crohn’s Disease journal July 2019
Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity text January 2015
Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics text January 2016
Whole Grain Oats Improve Insulin Sensitivity and Plasma Cholesterol Profile and Modify Gut Microbiota Composition in C57BL/6J Mice journal December 2014
Bovine Colostrum Modulates Myeloablative Chemotherapy–Induced Gut Toxicity in Piglets journal May 2015
NKT Cell–Deficient Mice Harbor an Altered Microbiota That Fuels Intestinal Inflammation during Chemically Induced Colitis journal October 2016
Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes journal January 2015
Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic) posted_content December 2012
Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen text January 2018
Structure and Diversity of the Bacterial Communities in the Acid and Thermophilic Crater-Lake of the Volcano “El Chichón”, Mexico text January 2018
Characterization of the salivary microbiome in patients with pancreatic cancer journal January 2015
A longitudinal study of the diabetic skin and wound microbiome journal January 2017
Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea journal January 2018
Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale journal January 2019
Biodegradation of thiocyanate by a native groundwater microbial consortium journal January 2019
A longitudinal study of the faecal microbiome and metabolome of periparturient mares journal January 2019
Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep journal January 2019
Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral journal January 2019

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