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1.
Nat Commun ; 12(1): 1926, 2021 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-33771992

RESUMEN

The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.


Asunto(s)
Microbioma Gastrointestinal/efectos de los fármacos , Infecciones por Helicobacter/tratamiento farmacológico , Helicobacter pylori/efectos de los fármacos , Aprendizaje Automático , Microbiota/efectos de los fármacos , Inhibidores de la Bomba de Protones/uso terapéutico , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Infecciones por Helicobacter/microbiología , Helicobacter pylori/fisiología , Humanos , Dinámica Poblacional , ARN Ribosómico 16S/genética , Estómago/microbiología
2.
Methods Mol Biol ; 2278: 195-208, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649958

RESUMEN

The genus Bifidobacterium constitutes one of the main groups of the human microbiota and some species have a long history of safe consumption supporting an excellent safety record. However, in the context of the increasing worldwide problems associate to the rise of pathogenic microorganisms with acquired resistance to antibiotics, the risk associated to the presence of antibiotic resistance determinants should always be a key starting point for the introduction of any microbial strain into the food chain. Bifidobacteria are not an exception and the presence of resistance to antibiotics is of interest since these microorganisms could potentially act as a reservoir of such resistances. In this context it is necessary to evaluate the presence of antibiotic resistance in any bifidobacterial strain to be included into the food chain. To this end, the first step is the determination of the antibiotic resistance pattern of the strain and the comparison with the susceptibility breakpoints for that species, allowing identifying the presence of atypical resistances in the strain. In this chapter we discuss the many efforts done to harmonize the methods used for the evaluation of antimicrobial susceptibility in the genus Bifidobacterium and the currently available guidelines. Moreover, we describe, in detail, the reference protocols used for evaluating the in vitro antimicrobial activity on bifidobacteria.


Asunto(s)
Antibacterianos/farmacología , Bifidobacterium/efectos de los fármacos , Farmacorresistencia Bacteriana , Humanos , Pruebas de Sensibilidad Microbiana/métodos , Microbiota/efectos de los fármacos , Probióticos
3.
J Insect Sci ; 21(1)2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-33560359

RESUMEN

The interest in using byproducts from agro-food industries as a rearing substrate for insects is increasing rapidly. We investigated the influence of byproducts of vegetal origin (okara-a byproduct of soy milk production, maize distillers with solubles, brewer's grains), used as rearing diet for black soldier fly larvae (BSFL), on the following parameters: biomass production, substrate reduction (SR), nutritional profile and in vitro digestibility, and larval gut microbiota. Hen diet was used as a control substrate. The highest larval biomass was collected on maize distillers, whereas the highest SR was observed on okara. The rearing substrate affected ash, ether extract, and chitin larval content. The BSFL reared on okara were characterized by a lower lauric acid content (17.6% of total fatty acids). Diets also influenced in vitro crude protein digestibility (%) for monogastrics, with the highest values for BSFL reared on maize distillers (87.8), intermediate for brewer's grains and okara BSFL, and the lowest for hen BSFL (82.7). The nutritive value for ruminants showed a lower Net Energy for lactation for BSFL reared on hen diet than okara and dried maize distillers BSFL. The different byproducts showed an influence on the larval gut microbiota, with a major bacterial complexity observed on larvae fed with the hen diet. The neutral detergent fiber concentration of dietary substrate was negatively correlated with Firmicutes and Actinobacteria relative abundance. Insects valorized byproducts converting them into high-value larval biomass to be used for feed production. The results evidenced the effects of the tested byproducts on the measured parameters, underling the chemical composition importance on the final insect meal quality.


Asunto(s)
Agricultura , Digestión , Dípteros/fisiología , Residuos Industriales/análisis , Microbiota , Fenómenos Fisiológicos Nutricionales de los Animales , Animales , Digestión/efectos de los fármacos , Dípteros/química , Dípteros/crecimiento & desarrollo , Dípteros/microbiología , Larva/química , Larva/crecimiento & desarrollo , Larva/microbiología , Larva/fisiología , Microbiota/efectos de los fármacos
4.
Microbiome ; 9(1): 32, 2021 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-33517907

RESUMEN

BACKGROUND: While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. RESULTS: Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. CONCLUSIONS: Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.


Asunto(s)
Entorno Construido , Microbiota , Boca/microbiología , Cepillado Dental , Adolescente , Adulto , Anciano , Farmacorresistencia Microbiana/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Humanos , Metagenoma/efectos de los fármacos , Metagenoma/genética , Microbiota/efectos de los fármacos , Microbiota/genética , Persona de Mediana Edad , Boca/efectos de los fármacos , Triclosán/farmacología , Adulto Joven
5.
Environ Toxicol Pharmacol ; 83: 103606, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33545380

RESUMEN

Heavy metal contamination of soil has become a public concern. Earthworms are key players in the functioning and service of soil ecosystems, with comprehension of their introduction in the polluted soil offering new insights into the protection of soil resources. In the present study, we evaluated the effects of earthworm (Eisenia fetida) introduction and Cd (0, 10, 30, and 60 mg kg-1 of Cd) exposure upon soil microbial community using 16S rRNA gene amplicon sequencing. Our research demonstrated that Gemmatimonadetes and Deinococcus-Thermus upregulated significantly, while Chryseolinea showed an obvious decreasing trend after earthworm introduction. In Cd contaminated soil, many genera exhibited a greater presence of Cd-dependent bacteria, namely Cd-tolerant bacteria such as Altererythrobacter and Luteimonas, and a decrease of sensitive bacteria, such as Amaricoccus and Haliangium. Moreover, functional prediction analysis of soil microbiota indicated that earthworm introduction and Cd exposure changed functional pathways of soil microorganisms. The results obtained in this study are beneficial for understanding soil microbial community impacted by earthworm, and for exploring Cd resistant or tolerant bacteria, with potentially significant findings for soil biodiversity and Cd bioremediation.


Asunto(s)
Cadmio/toxicidad , Microbiota/efectos de los fármacos , Oligoquetos , Contaminantes del Suelo/toxicidad , Animales , Bacterias/efectos de los fármacos , Bacterias/genética , Microbiota/genética , ARN Ribosómico 16S , Microbiología del Suelo
6.
Microbiome ; 9(1): 47, 2021 02 17.
Artículo en Inglés | MEDLINE | ID: mdl-33597039

RESUMEN

BACKGROUND: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. RESULTS: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development. CONCLUSIONS: The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.


Asunto(s)
Microbiota , Moraxella/genética , Moraxella/aislamiento & purificación , Propionibacteriaceae/genética , Propionibacteriaceae/aislamiento & purificación , Piel/microbiología , Adulto , Anciano , Antibacterianos/farmacología , China/etnología , Farmacorresistencia Microbiana/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Grupos Étnicos , Femenino , Genes Bacterianos/efectos de los fármacos , Humanos , Masculino , Metagenómica , Microbiota/efectos de los fármacos , Microbiota/genética , Persona de Mediana Edad , Moraxella/efectos de los fármacos , América del Norte/etnología , Propionibacteriaceae/efectos de los fármacos , Staphylococcus/efectos de los fármacos , Staphylococcus/genética , Staphylococcus/aislamiento & purificación , Simbiosis , Adulto Joven
7.
Int J Food Microbiol ; 343: 109086, 2021 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-33631605

RESUMEN

The importance of leaf integrity, i.e. the effects of bruising (mechanical damage), and sanitisation with peroxyacetic acid (PAA) on bacterial communities of ready-to-eat baby spinach remains unclear. Two shelf-life studies were conducted at 4 °C to investigate the effect of bruising and sanitisation on the growth of spoilage microorganisms. In the first experiment, both bruising treatments (100% and 40% of leaves) halved shelf life to 12 d, whereas intact leaves had a shelf-life of 23 d. Bruising had no influence on bacterial diversity during shelf-life, though some differences in the relative abundance of minor genera were observed. Pseudomonas and Pantoea were the most dominant bacterial genera, regardless of bruising treatment. High throughput amplicon sequencing also identified other spoilage bacteria including Chryseobacterium, Stenotrophomonas, Bacillus, Sphingobacterium, Erwinia and Flavobacterium. In the second experiment, washing of intact baby spinach with a sanitiser (80 mg/L: PAA) reduced microbial load as determined by aerobic plate count but did not immediately affect the presence/relative abundance of most of the genera of spoilage bacteria observed. During shelf-life, the bacterial diversity of sanitised leaves was significantly lower than on water-washed leaves. Although sanitisation resulted in a higher initial log reduction in microbial load compared to control (portable tap water), sanitisation did not extend the shelf life of baby spinach (23 d). Sanitised spinach had reduced bacterial diversity however, by the end of shelf life, both sanitised and water-washed spinach was dominated by Pseudomonas and Pantoea spoilage bacteria. This study demonstrated for the first time that the shorter shelf life of bruised leaves was related to faster microbial growth rather than changes in bacterial diversity or community composition.


Asunto(s)
Desinfectantes/farmacología , Almacenamiento de Alimentos/métodos , Microbiota/efectos de los fármacos , Ácido Peracético/farmacología , Spinacia oleracea/microbiología , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/crecimiento & desarrollo , Bacterias/aislamiento & purificación , Recuento de Colonia Microbiana , Microbiología de Alimentos , Hojas de la Planta/microbiología , Agua/farmacología
8.
Medicine (Baltimore) ; 100(1): e24059, 2021 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-33429768

RESUMEN

ABSTRACT: Microbiota plays an important role in many diseases including inflammatory bowel diseases. Inflammatory bowel disease patients can have concurrent irritable bowel syndrome symptoms similar to those associated with a flare. The potential role of gut dysbiosis in the pathogenesis of inflammatory bowel disease provides a rationale for treating such patients with rifaximin. This study aimed to assess the efficacy of rifaximin in the management of irritable bowel syndrome-like symptoms (bloating, abdominal pain, stool consistency) and quality of life in patients with Crohn's disease in remission.The present study included 86 patients with Crohn's disease in remission (fecal calprotectin <50 µg/g, C-reactive protein <0.5 mg/dL, simple endoscopic score for Crohn's disease <2) and associated irritable bowel syndrome-like symptoms (bloating, abdominal pain, diarrhea). These patients were randomly assigned to rifaximin treatment group (44 patients) and the control group (42 patients). Besides the baseline inflammatory bowel disease treatment and antispasmodics (as needed), patients in the rifaximin treatment group received 3 repeated courses of treatment, each course being represented by 1200 mg/d of rifaximin for 10 days and 20 days free of treatment (3 months consecutively); patients in the control group also received antispamodics as needed and were observed for 3 months.Monthly analyses of bloating score, abdominal pain score, stool consistency score, and quality of life score showed significant improvement after treatment in the rifaximin group in contrast with control group. Significantly more patients in the rifaximin group than in the control group met the criteria for adequate improvement of bloating score after 3 months of treatment (59.09% vs 19.04%, P = .01), adequate improvement of abdominal pain score (54.5% vs 21.4%, P = .04), stool consistency score (34.09% vs 14.2%, P = .03), and quality of life score (70.4% vs 21.4%, P < .001).Rifaximin in a dose of 1200 mg/d, 10 d/mo, 3 months consecutively is an effective medication for concurrent irritable bowel syndrome-like symptoms in patients with Crohn's disease in remission.


Asunto(s)
Enfermedad de Crohn/tratamiento farmacológico , Rifaximina/normas , Dolor Abdominal/tratamiento farmacológico , Adulto , Proteína C-Reactiva/análisis , Enfermedad de Crohn/complicaciones , Endoscopía/métodos , Heces , Femenino , Fármacos Gastrointestinales/farmacología , Fármacos Gastrointestinales/normas , Fármacos Gastrointestinales/uso terapéutico , Humanos , Complejo de Antígeno L1 de Leucocito/análisis , Masculino , Microbiota/efectos de los fármacos , Persona de Mediana Edad , Remisión Espontánea , Rifaximina/farmacología , Rifaximina/uso terapéutico
9.
Ecotoxicol Environ Saf ; 210: 111874, 2021 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-33421723

RESUMEN

Given the high content of Ca2+ in waste paper recycling wastewater, the anaerobic granular sludge (AnGS) undergoes calcification during wastewater treatment and affects the treatment efficiency. To restore the activity of calcified AnGS and improve the performance of AnGS, four types of N-acyl-homoserine lactones (AHLs) were added to the AnGS system while papermaking wastewater treatment. The addition of N-butyryl-DL-homoserine lactone(C4-HSL) and N-octanoyl-DL-homoserine lactone (C8-HSL) had an inhibitory affect the COD removal efficiency and SMA of sludge at the inception. The addition of N-hexanoyl-L-homoserine lactone (C6-HSL) has no obvious effect on the COD removal efficiency, but can improve the SMA of sludge more obviously. The addition of N-(ß-ketocaproyl)-DL-homoserine lactone (3O-C6-HSL) can increased COD removal efficiency and promoted SMA together obviously. The addition of C6-HSL and 3O-C6-HSL can increase volatile suspended solid (VSS)/total suspended solid (TSS), and regulate extracellular polymeric substance (EPS) secretion in AnGS. Analysis of microbial sequencing revealed changes in the microbial community structure following AHL addition, which enhanced the methane metabolism pathway in sludge. The addition of C6-HSL, C8-HSL, and 3O-C6-HSL increased Methanosaeta population, thus increasing the aceticlastic pathway in sludge. Thus, exogenous AHLs can play an important role in regulating microbial community structure, and in improving the performance of AnGS.


Asunto(s)
Lactonas/administración & dosificación , Microbiota/efectos de los fármacos , Aguas del Alcantarillado , Anaerobiosis , Matriz Extracelular de Sustancias Poliméricas/metabolismo , Metano/metabolismo , Papel , Aguas Residuales
10.
Ecotoxicol Environ Saf ; 208: 111724, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-33396055

RESUMEN

In recent years, in order to promote animal growth and reduce the risk of disease, a variety of antibiotics are frequently added to the animal feed of livestock and poultry. However, these antibiotics can not be fully digested by animals and most of them are excreted with feces, consequently causing the enrichment of antibiotic resistance genes (ARGs) and huge environmental risks. Nowadays, composting is a better option to solve these problems. Accordingly, this study explored the effects of co-composting swine manure with different inoculants dominated by Phanerochaete chrysosporium (p), Aspergillus niger (a), and Bacillus licheniformis (b) on the simultaneous removal of multiple antibiotics and resistance genes and evolution of the bacterial community. The results showed that the highest removal extent of tetracycline and oxytetracycline occurred in pile D (p:b:a=1:5:5, biomass) reaching 89.2% and 87.8%, respectively, while the highest removal extent of doxycycline and enrofloxacin occurred in pile A (p:b:a=1:0:0, biomass) reaching 98.6% and 89%, respectively. Compared with the levels in pile B (control check), in pile D, ARGs, except those for sulfonamides, decreased by 1.059 × 10-3-6.68 × 10-2 gene copies/16S rRNA copies. Inoculation with p alone effectively reduced intI1 and intI2. Canonical correspondence analysis (CCA) that microbial community structure evolution had a greater influence on ARGs than environmental factors. In summary, this study provided a feasible way to efficiently remove the antibiotics and antibiotic resistance genes in pig manure.


Asunto(s)
Antibacterianos/análisis , Farmacorresistencia Microbiana/genética , Estiércol/microbiología , Alimentación Animal/análisis , Animales , Antibacterianos/metabolismo , Bacterias/efectos de los fármacos , Compostaje/métodos , Genes Bacterianos , Ganado , Microbiota/efectos de los fármacos , Oxitetraciclina/farmacología , ARN Ribosómico 16S , Porcinos , Tetraciclina/farmacología
11.
Appl Environ Microbiol ; 87(7)2021 03 11.
Artículo en Inglés | MEDLINE | ID: mdl-33452033

RESUMEN

Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a two-by-two factorial design: (i) location (upstream or downstream of contaminating tributary), and (ii) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.IMPORTANCE Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study, in combination with previously published work on this same ecosystem, are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health, which currently does not include assessments of the microbiome.


Asunto(s)
Bacterias/aislamiento & purificación , Metales/efectos adversos , Microbiota/efectos de los fármacos , Ríos/microbiología , Contaminantes Químicos del Agua/efectos adversos , Colorado , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis
12.
Microbiome ; 9(1): 14, 2021 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-33436067

RESUMEN

BACKGROUND: The ozonation of biofilters is known to alleviate clogging and pressure drop issues while maintaining removal performances in biofiltration systems treating gaseous volatile organic compounds (VOCs). The effects of ozone on the biofilter microbiome in terms of biodiversity, community structure, metabolic abilities, and dominant taxa correlated with performance remain largely unknown. METHODS: This study investigated two biofilters treating high-concentration toluene operating in parallel, with one acting as control and the other exposed to low-dosage (200 mg/m3) ozonation. The microbial community diversity, metabolic rates of different carbon sources, functional predictions, and microbial co-occurrence networks of both communities were examined. RESULTS: Consistently higher biodiversity of over 30% was observed in the microbiome after ozonation, with increased overall metabolic abilities for amino acids and carboxylic acids. The relative abundance of species with reported stress-tolerant and biofilm-forming abilities significantly increased, with a consortium of changes in predicted biological pathways, including shifts in degradation pathways of intermediate compounds, while the correlation of top ASVs and genus with performance indicators showed diversifications in microbiota responsible for toluene degradation. A co-occurrence network of the community showed a decrease in average path distance and average betweenness with ozonation. CONCLUSION: Major degrading species highly correlated with performance shifted after ozonation. Increases in microbial biodiversity, coupled with improvements in metabolizing performances of multiple carbon sources including organic acids could explain the consistent performance commonly seen in the ozonation of biofilters despite the decrease in biomass, while avoiding acid buildup in long-term operation. The increased presence of stress-tolerant microbes in the microbiome coupled with the decentralization of the co-occurrence network suggest that ozonation could not only ameliorate clogging issues but also provide a microbiome more robust to loading shock seen in full-scale biofilters. Video abstract.


Asunto(s)
Filtración/métodos , Microbiota/efectos de los fármacos , Ozono/farmacología , Biopelículas/efectos de los fármacos , Biomasa , Tolueno
13.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Artículo en Inglés | MEDLINE | ID: mdl-33472859

RESUMEN

The COVID-19 pandemic has the potential to affect the human microbiome in infected and uninfected individuals, having a substantial impact on human health over the long term. This pandemic intersects with a decades-long decline in microbial diversity and ancestral microbes due to hygiene, antibiotics, and urban living (the hygiene hypothesis). High-risk groups succumbing to COVID-19 include those with preexisting conditions, such as diabetes and obesity, which are also associated with microbiome abnormalities. Current pandemic control measures and practices will have broad, uneven, and potentially long-term effects for the human microbiome across the planet, given the implementation of physical separation, extensive hygiene, travel barriers, and other measures that influence overall microbial loss and inability for reinoculation. Although much remains uncertain or unknown about the virus and its consequences, implementing pandemic control practices could significantly affect the microbiome. In this Perspective, we explore many facets of COVID-19-induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome's influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.


Asunto(s)
/microbiología , Hipótesis de la Higiene , Microbiota , Anciano , Antiinfecciosos/uso terapéutico , Ingestión de Alimentos , Femenino , Humanos , Lactante , Control de Infecciones/métodos , Masculino , Microbiota/efectos de los fármacos , Embarazo
14.
Microbiome ; 9(1): 29, 2021 01 27.
Artículo en Inglés | MEDLINE | ID: mdl-33504360

RESUMEN

BACKGROUND: Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets. RESULTS: The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 108 16S rRNA gene copies ng-1 DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential. CONCLUSIONS: Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.


Asunto(s)
Antiinfecciosos/farmacología , Ascomicetos/efectos de los fármacos , Ascomicetos/genética , Farmacorresistencia Microbiana/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Microbiota/efectos de los fármacos , Microbiota/genética , Colistina/farmacología , Glicina/análogos & derivados , Glicina/farmacología , Pirazinas/farmacología , ARN Ribosómico 16S/genética , Tetraciclina/farmacología
15.
Ecotoxicol Environ Saf ; 207: 111310, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32937228

RESUMEN

Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.


Asunto(s)
Acuicultura , Farmacorresistencia Microbiana/genética , Microbiota/fisiología , Bacterias/efectos de los fármacos , Bacteriófagos/efectos de los fármacos , Bacteriófagos/genética , China , Cultura , Genes Bacterianos/efectos de los fármacos , Humanos , Metagenómica , Microbiota/efectos de los fármacos
16.
Chemosphere ; 262: 128053, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33182130

RESUMEN

Nowadays, more and more attention is focused on the environmental harm brought by the wide production and use of carbon nanotubes. In this study, the metabolic function of sediment microbial community was investigated after unfunctionalized or functionalized multi-walled carbon nanotubes (MWCNTs) were incorporated. The surface functional groups on the studied functionalized MWCNTs in this work were hydroxyl, carboxyl, and amino, respectively. The metabolic functional diversity was determined by Biolog EcoPlates after one-month exposure to MWCNTs. Incorporating 0.5 wt% amino functionalized MWCNTs significantly decreased the microbial activity and diversity, and all types of MWCNTs caused great inhibition on the microbial metabolism at the dosage of 2.0 wt%. The sediment microbes preferred polymers and amino acids. Principal component and similarity analysis indicated that the microbial carbon metabolism was more affected by the MWCNT dosage compared with the functionalization, and 2.0 wt% amino functionalized MWCNTs made the greatest difference in metabolic function of sediment microbial community. These consequences may help to assess the environmental risks of MWCNTs from the aspect of ecological relevance of sediment microbial community.


Asunto(s)
Sedimentos Geológicos/microbiología , Microbiota/efectos de los fármacos , Nanotubos de Carbono/toxicidad , Ríos/microbiología , Contaminantes Químicos del Agua/toxicidad , Sedimentos Geológicos/química , Modelos Teóricos , Nanotubos de Carbono/química , Ríos/química , Propiedades de Superficie , Contaminantes Químicos del Agua/química
17.
Chemosphere ; 263: 127994, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32828062

RESUMEN

Anthropogenic salinisation is becoming an increasing global issue for freshwater ecosystems, leading to serious biodiversity loss and ecosystem degradation. While the effect of anthropogenic salinisation on freshwater ecosystems has been intensively studied in recent years, most studies focus on salinisation effects on the individual or single groups of organisms without considering the effect on the ecosystem levels, such as diversity and trophic links. Therefore, we conducted a long-term field survey from May 2009 to August 2016 at 405 sites in northeast China to investigate the effect of a gradient of salinisation on community diversity, functional diversity and trophic links in mountain streams. Samples of water chemistry, periphyton, macroinvertebrates and fish were collected. Our results showed that as anthropogenic salinisation increased, Ca2+, Mg2+, HCO3- and SO42- exhibited significant increases (p < 0.05). These increased ions caused decreases in taxonomic evenness and biotic integrity, but an increase in the beta diversity for periphyton and macroinvertebrates, and a slight increase in the evenness of fish. The increased salinisation resulted in the extirpation of salt-sensitive taxa and declines in macroinvertebrate functional richness and functional redundancy, which consequently led to simplified trophic links. Our results implied that if salt-tolerant taxa in high salinisation sites were not functionally redundant with less tolerant taxa, alterations of their functional composition probably decrease the stability of ecosystem functions. Overall, our study suggests that the ongoing anthropogenic salinisation is posing serious threats to biodiversity and trophic links in river ecosystems, and should be considered in future river restoration and biodiversity conservation.


Asunto(s)
Organismos Acuáticos/efectos de los fármacos , Biodiversidad , Plomo/toxicidad , Microbiota/efectos de los fármacos , Contaminantes Químicos del Agua/toxicidad , Animales , China , Ecosistema , Agua Dulce , Invertebrados/clasificación , Plomo/análisis , Características de la Residencia , Ríos/química , Contaminantes Químicos del Agua/análisis
18.
Chemosphere ; 262: 127822, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32799144

RESUMEN

In this research, for the first time, three kinds of landfill leachate (young (YL), mature (ML) and mixed (MYL) leachate) were treated in a semi-aerobic aged refuse biofilter (SAARB) to compare the effectiveness of, and microbial changes in, this biofilter when treating leachates that have significantly different characteristics. The SAARB achieved stable removal of organic matter from all three leachates and reduced the concentrations of aromatic substances. The best treatment was achieved with YL, followed in order by MYL and ML. The removal of nitrogen from all three leachates by the SAARB was particularly significant. The microbial abundance and diversity in the media of the SAARB changed after treatment of the three leachates, and the order of change from small to large was ML# < MYL# < YL#. The microbial communities were mainly affected by (and negatively correlated to) the relative content of refractory organics in leachate. Proteobacteria was the dominant microorganism. Deinococcus-thermus responded most to the quality of leachate being treated, increasing in relative abundance as the content of refractory organics increased. This was opposite to the response of Chloroflexi. In YL# the dominant species at the genus level was Thauera, and in ML# the dominant species were Truepera and Iodidimonas. The microbial activity and metabolic intensity were enhanced after treatment of the different leachates. The expression of nitrification-related genes was the strongest and the total abundance was the highest when YL was treated. This study promotes the optimization and application of SAARB.


Asunto(s)
Reactores Biológicos/microbiología , Microbiota/efectos de los fármacos , Contaminantes Químicos del Agua/toxicidad , Residuos de Alimentos , Nitrógeno , Eliminación de Residuos , Contaminantes Químicos del Agua/análisis
19.
Chemosphere ; 262: 127840, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32763570

RESUMEN

This work assessed the effect of the antibiotics trimethoprim (TMP) and sulfamethoxazole (SMX) on the granulation process, microbiology, and organic matter and nutrient removal of an aerobic granular sludge (AGS) system. In addition, after the maturation stage, the impact of the redox mediator anthraquinone-2,6-disulfonate (AQDS) (25 µM) on the biotransformation of the antibiotics was evaluated. The reactor R1 was maintained as a control, and the reactor R2 was supplemented with TMP and SMX (200 µg L-1). The ability to remove C, N, and P was similar between the reactors. However, the structural integrity of the AGS was impaired by the antibiotics. Low TMP (∼30%) and SMX (∼60%) removals were achieved when compared to anaerobic or floccular biomass aerobic systems. However, when the system was supplemented with AQDS, an increase in the removal of TMP (∼75%) and SMX (∼95%) was observed, possibly due to the catalytic action of the redox mediator on cometabolic processes. Regarding the microbial groups, whereas Proteobacteria and Bacterioidetes increased, Planctomycetes decreased in both reactors. However, TMP and SMX presence seemed to inhibit or favor some genera during the formation of the granules, possibly due to their bactericidal action.


Asunto(s)
Microbiota/efectos de los fármacos , Sulfametoxazol/toxicidad , Trimetoprim/toxicidad , Eliminación de Residuos Líquidos , Antibacterianos , Bacterias/efectos de los fármacos , Biomasa , Aguas del Alcantarillado , Sulfametoxazol/química , Trimetoprim/química , Microbiología del Agua
20.
Chemosphere ; 262: 127828, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32763579

RESUMEN

Cadmium (Cd) pollution is a widespread environmental problem that decreases crop production, destroys the microbial ecology of soil, and poses a severe risk to human health. Organo-chemical amendment is a cost-effective, eco-friendly, and community-acceptable widely applied an in situ technique for metal-contaminated farmland. In this study, we mixed lime, zeolite, calcium magnesium phosphate fertilizer, and biochar in a mixture ratio of 71:23:5:1 to form a mixed amendment. Field and laboratory experiments were conducted to study the effects of the mixed amendment on soil exchangeable Cd content, plant Cd accumulation, and soil microbial community. It was found that the application of 0.5% mixed amendment decreased exchangeable soil Cd by more than 85% and 64% in wheat and rice season, respectively, compared with control (CK), without increasing pH. Moreover, the application of 0.5% mixed amendment decreased Cd accumulation in grains by 22.9% and 41.2% in wheat and rice season, respectively, compared to CK. The result of phospholipid fatty acids (PLFAs) shows that the level of soil microbial diversity and species richness under mixed amendment treatments were higher than in lime treatment, indicating more copiotrophic conditions and faster rate of nutrient turnover in mixed amendment than pure lime treatment. Hence, it concluded that the mixed amendment has a strong effect on fixing exchangeable soil Cd and reducing the accumulation of Cd in crops. Finally, it was observed that the mixed amendment improved the soil microbial community structure and accelerate the rate of nutrient turnover by microbes under this favorable condition comparative to individual treatments.


Asunto(s)
Cadmio/química , Microbiota/efectos de los fármacos , Microbiología del Suelo , Contaminantes del Suelo/química , Agricultura/métodos , Cadmio/análisis , Cadmio/toxicidad , Compuestos de Calcio , Carbón Orgánico , Productos Agrícolas , Contaminación Ambiental , Restauración y Remediación Ambiental/métodos , Fertilizantes , Humanos , Microbiota/fisiología , Oryza/efectos de los fármacos , Óxidos , Fosfatos , Rotación , Suelo/química , Contaminantes del Suelo/análisis , Contaminantes del Suelo/toxicidad , Triticum
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