Avian MHC Evolution in the Era of Genomics: Phase 1.0

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.

Download Full-text

Long-term inorganic fertilizer use influences bacterial communities in Mollisols of Northeast China based on high-throughput sequencing and network analyses

Archives of Agronomy and Soil Science ◽

10.1080/03650340.2018.1563685 ◽

2019 ◽

Vol 65 (10) ◽

pp. 1331-1340 ◽

Cited By ~ 4

Author(s):

Zhenhua Yu ◽

Xiaojing Hu ◽

Dan Wei ◽

Junjie Liu ◽

Baoku Zhou ◽

...

Keyword(s):

High Throughput ◽

Bacterial Communities ◽

Northeast China ◽

High Throughput Sequencing ◽

Inorganic Fertilizer ◽

Fertilizer Use ◽

Network Analyses

Download Full-text

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation

Applied and Environmental Microbiology ◽

10.1128/aem.02885-17 ◽

2018 ◽

Vol 84 (9) ◽

Cited By ~ 15

Author(s):

Bing Li ◽

Wei-Min Wu ◽

David B. Watson ◽

Erick Cardenas ◽

Yuanqing Chao ◽

...

Keyword(s):

Network Analysis ◽

High Throughput ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Ecological Niches ◽

Content Type ◽

Oak Ridge ◽

Α Diversity ◽

Before And After

ABSTRACTA site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilizedin situthrough intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A pairedttest indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion.Castellaniellahad the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing generaGeothrix,Desulfovibrio,Ferribacterium, andGeobacterdecreased significantly, whereas the denitrifyingAcidovoraxabundance increased significantly after groundwater invasion. Additionally, seven genera, i.e.,Castellaniella,Ignavibacterium,Simplicispira,Rhizomicrobium,AcidobacteriaGp1,AcidobacteriaGp14, andAcidobacteriaGp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCEHigh-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.

Download Full-text

High-throughput sequencing reveals miRNA effects on the primary and secondary production properties in long-term subcultured Taxus cells

Frontiers in Plant Science ◽

10.3389/fpls.2015.00604 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 12

Author(s):

Meng Zhang ◽

Yanshan Dong ◽

Lin Nie ◽

Mingbo Lu ◽

Chunhua Fu ◽

...

Keyword(s):

High Throughput ◽

Secondary Production ◽

High Throughput Sequencing

Download Full-text

High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00789-12 ◽

2012 ◽

Vol 56 (11) ◽

pp. 5811-5820 ◽

Cited By ~ 252

Author(s):

Fiona Fouhy ◽

Caitriona M. Guinane ◽

Seamus Hussey ◽

Rebecca Wall ◽

C. Anthony Ryan ◽

...

Keyword(s):

Gut Microbiota ◽

Antibiotic Treatment ◽

High Throughput ◽

High Throughput Sequencing ◽

Short Term ◽

Parenteral Antibiotic ◽

Content Type ◽

Combined Use ◽

Cessation Of Treatment

ABSTRACTThe infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA andrpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions ofProteobacteria(P= 0.0049) and significantly lower proportions ofActinobacteria(P= 0.00001) (and the associated genusBifidobacterium[P= 0.0132]) as well as the genusLactobacillus(P= 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, theProteobacterialevels remained significantly higher in the treated infants (P= 0.0049), but theActinobacteria,Bifidobacterium, andLactobacilluslevels had recovered and were similar to those in the control samples. Despite this recovery of totalBifidobacteriumnumbers,rpoB-targeted pyrosequencing revealed that the number of differentBifidobacteriumspecies present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.

Download Full-text

GenBank is a reliable resource for 21st century biodiversity research

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1911714116 ◽

2019 ◽

Vol 116 (45) ◽

pp. 22651-22656 ◽

Cited By ~ 34

Author(s):

Matthieu Leray ◽

Nancy Knowlton ◽

Shian-Lei Ho ◽

Bryan N. Nguyen ◽

Ryuji J. Machida

Keyword(s):

Phylogenetic Analysis ◽

Global Change ◽

High Throughput ◽

High Throughput Sequencing ◽

Environmental Dna ◽

Taxonomic Resolution ◽

Biodiversity Research ◽

Animal Diversity ◽

Mitochondrial Sequences ◽

The Many

Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable. Thus, identifying these sequences typically relies on comparisons with sequences from genetic databases, particularly GenBank. While concerns have been raised about biases and inaccuracies in laboratory and analytical methods, comparatively little attention has been paid to the taxonomic reliability of GenBank itself. Here we analyze the metazoan mitochondrial sequences of GenBank using a combination of distance-based clustering and phylogenetic analysis. Because of their comparatively rapid evolutionary rates and consequent high taxonomic resolution, mitochondrial sequences represent an invaluable resource for the detection of the many small and often undescribed organisms that represent the bulk of animal diversity. We show that metazoan identifications in GenBank are surprisingly accurate, even at low taxonomic levels (likely <1% error rate at the genus level). This stands in contrast to previously voiced concerns based on limited analyses of particular groups and the fact that individual researchers currently submit annotated sequences to GenBank without significant external taxonomic validation. Our encouraging results suggest that the rapid uptake of DNA-based approaches is supported by a bioinformatic infrastructure capable of assessing both the losses to biodiversity caused by global change and the effectiveness of conservation efforts aimed at slowing or reversing these losses.

Download Full-text

Many roads to bacterial generalism

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa240 ◽

2020 ◽

Vol 97 (1) ◽

Author(s):

Terrence H Bell ◽

Thomas Bell

Keyword(s):

High Throughput ◽

Functional Role ◽

High Throughput Sequencing ◽

Temperature Tolerance ◽

Functional Potential ◽

Environmental Manipulation ◽

New Approaches ◽

Different Types ◽

The Many

ABSTRACT The fundamental niches of bacteria can be defined along many environmental axes, including temperature tolerance and resources consumed, while interactions with other organisms can constrain (e.g. competition) or enlarge (e.g. cross-feeding) realized niches. Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements, which can then be linked to their functional role in an ecosystem. We show how these terms are applied to bacteria, make predictions about how the type and extent of generalism displayed by an organism relates to its functional potential and discuss the value of collecting different types of generalist bacteria. We believe that new approaches that take advantage of both high-throughput sequencing and environmental manipulation can allow us to understand the many types of generalism found within both cultivated and yet-to-be-cultivated bacteria.

Download Full-text