This study explored the short-term planktonic microbial community structure and resilience in Lake Lanier (GA, USA) while simultaneously evaluating the technical aspects of identifying taxa via 16S ...rRNA gene amplicon and metagenomic sequence data. 16S rRNA gene amplicons generated from four temporally discrete samples were sequenced with 454 GS-FLX-Ti yielding ∼40,000 rRNA gene sequences from each sample and representing ∼300 observed OTUs. Replicates obtained from the same biological sample clustered together but several biases were observed, linked to either the PCR or sequencing-preparation steps. In comparisons with companion whole-community shotgun metagenome datasets, the estimated number of OTUs at each timepoint was concordant, but 1.5 times and ∼10 times as many phyla and genera, respectively, were identified in the metagenomes. Our analyses showed that the 16S rRNA gene captures broad shifts in community diversity over time, but with limited resolution and lower sensitivity compared to metagenomic data. We also identified OTUs that showed marked shifts in abundance over four close timepoints separated by perturbations and tracked these taxa in the metagenome vs. 16S rRNA amplicon data. A strong summer storm had less of an effect on community composition than did seasonal mixing, which revealed a distinct succession of organisms. This study provides insights into freshwater microbial communities and advances the approaches for assessing community diversity and dynamics in situ.
When it comes to fitting simple allometric slopes through measurement data, evolutionary biologists have been torn between regression methods. On the one hand, there is the ordinary least squares ...(OLS) regression, which is commonly used across many disciplines of biology to fit lines through data, but which has a reputation for underestimating slopes when measurement error is present. On the other hand, there is the reduced major axis (RMA) regression, which is often recommended as a substitute for OLS regression in studies of allometry, but which has several weaknesses of its own. Here, we review statistical theory as it applies to evolutionary biology and studies of allometry. We point out that the concerns that arise from measurement error for OLS regression are small and straightforward to deal with, whereas RMA has several key properties that make it unfit for use in the field of allometry. The recommended approach for researchers interested in allometry is to use OLS regression on measurements taken with low (but realistically achievable) measurement error. If measurement error is unavoidable and relatively large, it is preferable to correct for slope attenuation rather than to turn to RMA regression, or to take the expected amount of attenuation into account when interpreting the data.
A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average ...Nucleotide Identity (ANI) help address this question by facilitating high resolution taxonomic analysis of thousands of genomes from diverse phylogenetic lineages. To scale to available genomes and beyond, we present FastANI, a new method to estimate ANI using alignment-free approximate sequence mapping. FastANI is accurate for both finished and draft genomes, and is up to three orders of magnitude faster compared to alignment-based approaches. We leverage FastANI to compute pairwise ANI values among all prokaryotic genomes available in the NCBI database. Our results reveal clear genetic discontinuity, with 99.8% of the total 8 billion genome pairs analyzed conforming to >95% intra-species and <83% inter-species ANI values. This discontinuity is manifested with or without the most frequently sequenced species, and is robust to historic additions in the genome databases.
Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary ...microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.
Abstract
The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the ...species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.
Summary
Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet‐uncultivated microorganisms from diverse environments. However, ...the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome‐assembled genomes (MAGs) represents >400 yet‐unnamed genomospecies, substantially increasing the number of high‐quality MAGs from freshwater lakes. We propose names for two novel species: ‘Candidatus Elulimicrobium humile’ (‘Ca. Elulimicrobiota’, ‘Patescibacteria’) and ‘Candidatus Aquidulcis frankliniae’ (‘Chloroflexi’). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat‐specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.
Lynch syndrome is the most common genetic predisposition for hereditary cancer but remains underdiagnosed. Large prospective observational studies have recently increased understanding of the ...effectiveness of colonoscopic surveillance and the heterogeneity of cancer risk between genotypes. The need for gene- and gender-specific guidelines has been acknowledged.
The European Hereditary Tumour Group (EHTG) and European Society of Coloproctology (ESCP) developed a multidisciplinary working group consisting of surgeons, clinical and molecular geneticists, pathologists, epidemiologists, gastroenterologists, and patient representation to conduct a graded evidence review. The previous Mallorca guideline format was used to revise the clinical guidance. Consensus for the guidance statements was acquired by three Delphi voting rounds.
Recommendations for clinical and molecular identification of Lynch syndrome, surgical and endoscopic management of Lynch syndrome-associated colorectal cancer, and preventive measures for cancer were produced. The emphasis was on surgical and gastroenterological aspects of the cancer spectrum. Manchester consensus guidelines for gynaecological management were endorsed. Executive and layperson summaries were provided.
The recommendations from the EHTG and ESCP for identification of patients with Lynch syndrome, colorectal surveillance, surgical management of colorectal cancer, lifestyle and chemoprevention in Lynch syndrome that reached a consensus (at least 80 per cent) are presented.
•Biomodulina T (InmunyVital®) modulates immune response and inflammation.•Biomodulina T (InmunyVital®) restores immunity and thymus size in children.•Biomodulina T (InmunyVital®) helps control ...multiple sclerosis.•Biomodulina T (InmunyVital®) reverses B and T cells immunosenescence.•Biomodulina T (InmunyVital®) restores immunity in cancer immunotherapy.
Biomodulina T (InmunyVital®) is a thymic factor that modulates immune response and inflammation. Biomodulina T stimulates the differentiation, maturation and proliferation of T cells. Additionally, Biomodulina T improves the ability of T cells to produce cytokines, therefore enhancing T lymphocyte function. Biomodulina T stimulates the thymus gland and, thus, promotes the recovery of normal thymus size in children with thymic hypoplasia and restores the functions of immunosenescent T cells in aging people.
In 1984 Rodriguez Martin RR established the laboratory of Biomodulators, where he created and developed an immunomodulatory thymic factor that he named “Biomodulina T.” The biological activity of Biomodulina T was demonstrated in several studies. An extensive series of preclinical toxicological studies were conducted and these studies demonstrated that Biomodulina T is an active and safe thymic factor.
Clinical trials were conducted with Biomodulina T in patients with immunodeficiency and infections, autoimmune diseases, older adults with recurrent respiratory infections, and cancer.
In 1994, we obtained the approval of Biomodulina T as an immunomodulatory drug.
This article identifies the milestones involved in the development of Biomodulina T. Since its discovery more than 35 years ago, reports show that Biomodulina T is a modulator of immune response and inflammation that is very useful for restoring the immune system in young and elderly people with immunodeficiencies, autoimmune diseases, and infections. Biomodulina T is also useful as an immunotherapeutic agent for improving immune responses in cancer and vaccines, for reversing immunosenescence and for improving healthspan in aging.
AimsHyperphosphorylated tau neuronal cytoplasmic inclusions (ht‐NCI) are the best protein correlate of clinical decline in Alzheimer's disease (AD). Qualitative evidence identifies ht‐NCI ...accumulating in the isodendritic core before the entorhinal cortex. Here, we used unbiased stereology to quantify ht‐NCI burden in the locus coeruleus (LC) and dorsal raphe nucleus (DRN), aiming to characterize the impact of AD pathology in these nuclei with a focus on early stages.MethodsWe utilized unbiased stereology in a sample of 48 well‐characterized subjects enriched for controls and early AD stages. ht‐NCI counts were estimated in 60‐μm‐thick sections immunostained for p‐tau throughout LC and DRN. Data were integrated with unbiased estimates of LC and DRN neuronal population for a subset of cases.ResultsIn Braak stage 0, 7.9% and 2.6% of neurons in LC and DRN, respectively, harbour ht‐NCIs. Although the number of ht‐NCI+ neurons significantly increased by about 1.9× between Braak stages 0 to I in LC (P = 0.02), we failed to detect any significant difference between Braak stage I and II. Also, the number of ht‐NCI+ neurons remained stable in DRN between all stages 0 and II. Finally, the differential susceptibility to tau inclusions among nuclear subdivisions was more notable in LC than in DRN.ConclusionsLC and DRN neurons exhibited ht‐NCI during AD precortical stages. The ht‐NCI increases along AD progression on both nuclei, but quantitative changes in LC precede DRN changes.
Stereological analysis of tau pathology in the locus coeruleus and dorsal raphe nucleus in early Alzheimer's disease demonstrate that early involvement of brain stem nuclei has important functional implications.
This article describes the first results obtained from the Surface Waves Investigation and Monitoring (SWIM) instrument carried by the China France Oceanography Satellite (CFOSAT), which was launched ...on October 29, 2018. SWIM is a Ku-band radar with a near-nadir scanning beam geometry. It was designed to measure the spectral properties of surface ocean waves. First, the good behavior of the instrument is illustrated. It is then shown that the nadir products (significant wave height, normalized radar cross section, and wind speed) exhibit an accuracy similar to standard altimeter missions, thanks to a new retracking algorithm, which compensates a lower sampling rate compared to standard altimetry missions. The off-nadir beam observations are analyzed in detail. The normalized radar cross section varies with incidence and wind speed as expected from previous studies presented in the literature. We illustrate that, in order to retrieve the wave spectra from the radar backscattering fluctuations, it is crucial to apply a speckle correction derived from the observations. Directional spectra of ocean waves and their mean parameters are then compared to wave model data at the global scale and to in situ data from a selection of case studies. The good efficiency of SWIM to provide the spectral properties of ocean waves in the wavelength range 70-500 m is illustrated. The main limitations are discussed, and the perspectives to improve the data quality are presented.
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