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The development of high throughput methods has enabled the study of hundreds of samples and metaproteomics is not the exception. However, the study of thousands of proteins of different organisms represents different challenges from the protein extraction to the bioinformatic analysis. Here, the sample preparation, protein extraction and protein purification for livestock microbiome research throughout metaproteomics are described. These methods are essential because the quality of the final protein pool depends on them. For that reason, the following workflow is a combination of different chemical and physical methods that intend an initial separation of the microbial organisms from the host cells and other organic materials, as well as the extraction of high concentrate pure samples., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The genus Ligilactobacillus encompasses species adapted to vertebrate hosts and fermented food. Their genomes encode adaptations to the host lifestyle. Reports of gut microbiota from chicken and turkey gastrointestinal tract have shown a high persistence of Ligilactobacillus aviarius along the digestive system compared to other species found in the same host. However, its adaptations to poultry as a host has not yet been described. In this work, the pan-genome of Ligilactobacillus aviarius was explored to describe the functional adaptability to the gastrointestinal environment. The core genome is composed of 1179 gene clusters that are present at least in one copy that codifies to structural, ribosomal and biogenesis proteins. The rest of the identified regions were classified into three different functional clusters of orthologous groups (clusters) that codify carbohydrate metabolism, envelope biogenesis, viral defence mechanisms, and mobilome inclusions. The pan-genome of Ligilactobacillus aviarius is a closed pan-genome, frequently found in poultry and highly prevalent across chicken faecal samples. The genome of L. aviarius codifies different clusters of glycoside hydrolases and glycosyltransferases that mediate interactions with the host cells. Accessory features, such as antiviral mechanisms and prophage inclusions, variate amongst strains from different GIT sections. This information provides hints about the interaction of this species with viral particles and other bacterial species. This work highlights functional adaptability traits present in L. aviarius that make it a dominant key member of the poultry gut microbiota and enlightens the convergent ecological relation of this species to the poultry gut environment., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors. Published by Elsevier B.V.)

Human papillomavirus can cause preinvasive, high-grade squamous intraepithelial lesions (HSILs) as precursors to cancer in the anogenital area, and the microbiome is suggested to be a contributing factor. Men who have sex with men (MSM) living with human immunodeficiency virus (HIV) have a high risk of anal cancer, but current screening strategies for HSIL detection lack specificity. Here, we investigated the anal microbiome to improve HSIL screening. We enrolled participants living with HIV, divided into a discovery (n = 167) and validation cohort (n = 46), and who were predominantly (93.9%) cisgender MSM undergoing HSIL screening with high-resolution anoscopy and anal biopsies. We identified no microbiome composition signatures associated with HSILs, but elevated levels of microbiome-encoded proteins producing succinyl coenzyme A and cobalamin were significantly associated with HSILs in both cohorts. Measurement of these candidate biomarkers alone in anal cytobrushes outperformed anal cytology as a diagnostic indicator for HSILs, increasing the sensitivity from 91.2% to 96.6%, the specificity from 34.1% to 81.8%, and reclassifying 82% of false-positive results as true negatives. We propose that these two microbiome-derived biomarkers may improve the current strategy of anal cancer screening., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community.

The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.

Background: Global Asthma Network (GAN) was established in 2012 as a development to the International Study of Asthma and Allergies in Childhood to improve asthma care globally., Objective: To survey asthma, allergic rhinitis and atopic dermatitis in primary and secondary school children and to investigate and evaluate its prevalence, severity, management and risk factors in Mexico., Methods: GAN Phase I is a cross-sectional, multicentre survey carried out in 15 centres corresponding to 14 Mexican cities throughout 2016-2019 using the validated Spanish language version of the GAN Phase I questionnaires. The questionnaires were completed by parents of 6-7-year-old primary school pupils (school children) and by 13-14-year-old adolescents., Results: A total of 35 780 school children and 41 399 adolescents participated. Wheezing ever prevalence was 26.2% (95% CI 25.8% to 26.7%) in school children and 23.9% (95% CI 23.4% to 24.3%) in adolescents. The corresponding frequencies for current wheeze were 10.2% (95% CI 9.9% to 10.5%) and 11.6% (95% CI 11.2% to 11.9%). In school children, the risk factors for current wheeze were rhinitis (OR 4.484; 95% CI 3.915% to 5.134%) and rash symptoms (OR 1.735; 95% CI 1.461% to 2.059%). For adolescents, rhinitis symptoms (OR 3.492; 95% CI 3.188% to 3.825%) and allergic rhinitis diagnosis (OR 2.144; 95% CI 1.787% to 2.572%) were the most significant. For both groups, there was a negative relation with centres' sea level altitude higher than 1500 m above mean sea level (p<0.005)., Conclusions: The most important risk factors for asthma symptoms in both age groups were the presence of rhinitis and rash symptoms or diagnosis. On the other hand, sea level altitude higher than 1500 metres was a protective factor., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Allergen immunotherapy (AIT) has a longstanding history and still remains the only disease-changing treatment for allergic rhinitis and asthma. Over the years 2 different schools have developed their strategies: the United States (US) and the European. Allergen extracts available in these regions are adapted to local practice. In other parts of the world, extracts from both regions and local ones are commercialized, as in Mexico. Here, local experts developed a national AIT guideline (GUIMIT 2019) searching for compromises between both schools., Methods: Using ADAPTE methodology for transculturizing guidelines and AGREE-II for evaluating guideline quality, GUIMIT selected 3 high-quality Main Reference Guidelines (MRGs): the European Academy of Allergy, Asthma and Immunology (EAACI) guideines, the S2k guideline of various German-speaking medical societies (2014), and the US Practice Parameters on Allergen Immunotherapy 2011. We formulated clinical questions and based responses on the fused evidence available in the MRGs, combined with local possibilities, patient's preference, and costs. We came across several issues on which the MRGs disagreed. These are presented here along with arguments of GUIMIT members to resolve them. GUIMIT (for a complete English version, Supplementary data) concluded the following., Results: Related to the diagnosis of IgE-mediated respiratory allergy, apart from skin prick testing complementary tests (challenges, in vitro testing and molecular such as species-specific allergens) might be useful in selected cases to inform AIT composition. AIT is indicated in allergic rhinitis and suggested in allergic asthma (once controlled) and IgE-mediated atopic dermatitis. Concerning the correct subcutaneous AIT dose for compounding vials according to the US school: dosing tables and formula are given; up to 4 non-related allergens can be mixed, refraining from mixing high with low protease extracts. When using European extracts: the manufacturer's indications should be followed; in multi-allergic patients 2 simultaneous injections can be given (100% consensus); mixing is discouraged. In Mexico only allergoid tablets are available; based on doses used in all sublingual immunotherapy (SLIT) publications referenced in MRGs, GUIMIT suggests a probable effective dose related to subcutaneous immunotherapy (SCIT) might be: 50-200% of the monthly SCIT dose given daily, maximum mixing 4 allergens. Also, a table with practical suggestions on non-evidence-existing issues, developed with a simplified Delphi method, is added. Finally, dissemination and implementation of guidelines is briefly discussed, explaining how we used online tools for this in Mexico., Conclusions: Countries where European and American AIT extracts are available should adjust AIT according to which school is followed., Competing Interests: All authors declared or they have no potential conflicts of interest. The following authors, indicated relations with the pharmaceutical industry: Dr. Larenas Linnemann reports personal fees from Allakos, Amstrong, 10.13039/100004325Astrazeneca, 10.13039/100001003Boehringer Ingelheim, 10.13039/100007560Chiesi, DBV Technologies, Grunenthal, 10.13039/100004330GSK, MEDA, Menarini, 10.13039/100007054MSD, 10.13039/100004336Novartis, 10.13039/100004319Pfizer, 10.13039/100004336Novartis, 10.13039/100004339Sanofi, Siegfried, 10.13039/100011110UCB, Gossamer, grants from 10.13039/100004319Sanofi, 10.13039/100004325Astrazeneca, Novartis, 10.13039/100011110UCB, GSK, 10.13039/100006259TEVA, 10.13039/100001003Boehringer Ingelheim, 10.13039/100007560Chiesi, Purina institute., outside the submitted work; Dr. Moncayo Coello reports personal fees from 10.13039/100004325AstraZeneca, personal fees from 10.13039/100004339Sanofi, personal fees from 10.13039/100004330Grünenthal, personal fees from 10.13039/100011218Sandoz, outside the submitted work; Dr. Partida-Gaytan reports personal fees from 10.13039/100012690Nestlé Nutrition Institute, personal fees from 10.13039/100004330GlaxoSmithKline Mexico, personal fees from Instituto Nacional de Pediatria, personal fees from Healthy Kids Polanco S.C., outside the submitted work., (© 2020 The Authors.)

Aims: This study evaluated the effects of DNA extraction method, DNA purification and pooling of PCR amplification products on the description of bacterial and archaeal diversity., Methods and Results: Soil DNA was extracted by the Power Soil DNA extraction kit and a customized Griffiths' protocol. Both methods are based on cell disruption by bead beating. In total, we used three soils and six independent extractions from each soil obtained by each of the two methods. Then, three of the six extracts of each treatment were further purified by spin columns filled with Sepharose 2B and polyvinylpolypyrrolidone (PVPP). The V4 hypervariable region of the 16S rRNA gene was amplified from each extract using the 515F/806R primer pair in four independent reactions. Three amplification products were combined and sequenced as a pooled sample, while the additional amplification product was sequenced individually. The resulting 72 amplification products were sequenced by Illumina MiSeq platform. DNA extraction method had a statistically significant effect on the estimation of the composition of microbial communities that might overwhelm differences in microbial communities from distinct soils. On the other hand, a further DNA purification step or pooling of PCR amplification products had a minor effect on the description of bacterial and archaeal communities., Conclusions: DNA extraction had the strongest effect on the description of bacterial and archaeal communities; low concentration of impurities, which allow PCR amplification, can still generate a minor additional bias, while PCR stochastic variability had the lowest effect., Significance and Impact of the Study: Although it is well known that methodological factors affect the description of microbial communities, the relative importance of each step is still unknown. The present study determined that of the factors tested, the DNA extraction method had the strongest effects on the description of bacterial and archaeal communities., (© 2019 The Society for Applied Microbiology.)

Background: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach., Results: The total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase., Conclusions: Our findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.

Background: In Mexico, allergen immunotherapy (AIT) and immunotherapy with hymenoptera venom (VIT) is traditionally practiced combining aspects of the European and American school. In addition, both types of extracts (European and American) are commercially available in Mexico. Moreover, for an adequate AIT/VIT a timely diagnosis is crucial. Therefore, there is a need for a widely accepted, up-to-date national immunotherapy guideline that covers diagnostic issues, indications, dosage, mechanisms, adverse effects and future expectations of AIT (GUIMIT 2019)., Method: With nationwide groups of allergists participating, including delegates from postgraduate training-programs in Allergy/Immunology-forming, the guideline document was developed according to the ADAPTE methodology: the immunotherapy guidelines from European Academy of Allergy and Clinical Immunology, German Society for Allergology and Clinical Immunology, The American Academy of Allergy, Asthma and Immunology and American College of Allergy, Asthma, and Immunology were selected as mother guidelines, as they received the highest AGREE-II score among international guidelines available; their evidence conforms the scientific basis for this document., Results: GUIMIT emanates strong or weak (suggestions) recommendations about practical issues directly related to in vivo or in vitro diagnosis of IgE mediated allergic diseases and the preparation and application of AIT/VIT and its adverse effects. GUIMIT finishes with a perspective on AIT modalities for the future. All the statements were discussed and voted on until > 80 % consensus was reached., Conclusions: A wide and diverse group of AIT/VIT experts issued transculturized, evidence-based recommendations and reached consensus that might improve and standardize AIT practice in Mexico.

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: ( i ) a physico-chemical characterization of the soil habitability after an exceptional rain event, ( ii ) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], ( iii ) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and ( iv ) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Background: The need for a national guideline, with a broad basis among specialists and primary care physicians was felt in Mexico, to try unifying asthma management. As several high-quality asthma guidelines exist worldwide, it was decided to select the best three for transculturation., Methods: Following the internationally recommended methodology for guideline transculturation, ADAPTE, a literature search for asthma guidelines, published 1-1-2007 through 31-12-2015 was conducted. AGREE-II evaluations yielded 3/40 most suitable for transculturation. Their compound evidence was fused with local reality, patient preference, cost and safety considerations to draft the guideline document. Subsequently, this was adjusted by physicians from 12 national medical societies in several rounds of a Delphi process and 3 face-to-face meetings to reach the final version., Results: Evidence was fused from British Thoracic Society Asthma Guideline 2014, Global Initiative on Asthma 2015, and Guía Española del Manejo del Asma 2015 (2016 updates included). After 3 Delphi-rounds we developed an evidence-based document taking into account patient characteristics, including age, treatment costs and safety and best locally available medication., Conclusions: In cooperation pulmonologists, allergists, ENT physicians, paediatricians and GPs were able to develop an evidence-based document for the prevention, diagnosis and treatment of asthma and its exacerbations in Mexico.

Cow's milk allergy (CMA) is an immune-based disease that has become an increasing problem. The diagnosis and management of CMA varies from one clinical setting to another and represents a challenge in pediatric practice. In addition, because nonallergic food reactions can be confused with CMA symptoms, there is an overdiagnosis of the disease. In response to these situations, pediatric specialties from recognized institutions throughout Latin America decided to develop a clinical guideline for diagnosis and management of cow's milk allergy. These guidelines include definitions, epidemiology, pathophysiology overview, clinical and evidencebased recommendations for the diagnosis and treatment of CMA. They also include prevention and prognosis sections and identify gaps in the current knowledge to be addressed through future research.

Objectives: To test which is the best treatment for chronic obstructive uropathy: urinary diversion using a conventional double-J ureteral stent or the metal thermo-expandable MemokathTM 051 prosthesis., Methods: We collected cost data of the insertion of a double-J stent taking into account preoperative and postoperative visits and surgery. Structural, medical, consumables and the prosthesis costs were considered. The estimated survival of the patient, number of spare stents and cost of each therapeutic measure were computed. Then, a simulation of the cost of inserting a MemokathTM 051 prosthesis was conducted, based on data of ureteral catheterization. We performed a decision tree and Cost Effectiveness economic analysis to measure the effectiveness of both health interventions., Results: Cost data of each procedure were: 1275.44 € for the double J catheter in a program of day case surgery (DCS), 4865.16 € for the metal thermo-expandable prosthesis as DCS, and 1424.52€for the double J stent with 1 day admission and 5014.24 € for the prosthesis with 1 day admission. The cost difference between ureteral stent and metal thermo-expandable prosthesis is 3589.72 € per treatment for the ureteral stent as DCS., Conclusions: Despite its high initial cost, the metal thermo-expandable prosthesis potentially offers economic advantages over the conventional double-J ureteral stent in the treatment of long evolution ureteral obstruction. After the third change of double-J stent, and if the patient survival is long enough, the metal prosthesis as DCS should be the most cost effective option.

In the context of a multidisciplinary approach for the diagnosis and treatment of ovarian cancer, the contribution of radiology includes the following four fundamental points: identification of the lesion, its characterization, study of its extension and evaluation of its evolution. This article describes the findings and key diagnostic elements in MDCT (Multidetector Computed Tomography) and MR (Magnetic Resonance), the contribution and indication of other technologies like PET (Positron Emission Tomography), and outlines the emergent techniques based on functional image analysis (dynamic contrast-enhanced MRI studies and MRI diffusion studies).

Several calibration settings of diffusion barrier charcoal canister (DBCC) detectors for measuring radon concentration in air were studied. A set of functions and graphs were developed for relations between radon concentration in air and adsorbed activity in DBCC, when calibrated in small chambers. Both the integration time for 10% of DBCC of a batch, and the radon adsorption coefficient for the activated charcoal used in these detectors, were determined. Thus, a semi-empirical expression for detector calibration was applied.