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1.
Medicine (Baltimore) ; 100(15): e25526, 2021 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-33847675

RESUMEN

RATIONALE: In some cases, autopsy is the first opportunity to find a previously unrecognized critical infection. Pathogens are identified by various methods, such as microscopic examination, special stains, culture tests, and immunohistochemistry. Here, we report a case of 16S ribosomal RNA (rRNA) gene sequencing using a postmortem formalin-fixed, paraffin-embedded (FFPE) tissue, which was useful for identifying pathogenic microbes. PATIENT CONCERNS: Autopsy was performed on an 87-year-old man who had chronic renal failure and had developed sepsis from a central venous catheter infection 10 days before his death. Prior to these events, von Meyenburg complexes (VMCs) were also found during regular checkups. DIAGNOSIS: Postmortem microscopic examination revealed acute purulent cholangitis with numerous microabscesses, accompanied by VMCs. Gram-negative rods were observed in some microabscesses, which were considered causative pathogens. INTERVENTIONS: 16S rRNA gene sequencing using postmortem FFPE tissue. OUTCOMES: Pseudomonas aeruginosa was identified, different from the one detected in the central venous catheter culture while alive. LESSONS: 16S rRNA gene sequencing is a useful tool for identifying pathogenic microbes in postmortem FFPE tissues. This technique may be useful for amplicon sizes of approximately 100 bp or less.


Asunto(s)
Enfermedades de las Vías Biliares/microbiología , Colangitis/microbiología , Hamartoma/microbiología , Pseudomonas aeruginosa , ARN Bacteriano/análisis , Enfermedad Aguda , Anciano de 80 o más Años , Autopsia , Resultado Fatal , Formaldehído , Humanos , Masculino , Ilustración Médica , Adhesión en Parafina , ARN Ribosómico 16S/análisis , Análisis de Secuencia de ARN
2.
Phytomedicine ; 86: 153561, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33857850

RESUMEN

BACKGROUND: Peritoneal dialysis (PD) is an acknowledged treatment for patients with irreversible kidney failure. The treatment usually causes peritoneal dialysis-related peritonitis (PDRP), a common complication of PD that can lead to inadequate dialysis, gastrointestinal dysfunction, and even death. Recent studies indicated that Fushen Granule (FSG), a Chinese herbal formula, improves the treatment of PD. However, the mechanism of how FSG plays its role in the improvement is still unclear. Gut microbiota has been closely related to the development of various diseases. We carried out a randomized controlled trial to assess whether FSG can modulate the gut microbiota during PDRP treatment. METHODS: Forty-two PDRP patients were recruited into the clinical trial, and they were randomly divided into control(CON), probiotics(PRO) or Fushen granule group(FSG). To check whether FSG improve the PD treatment, we assessed the clinical parameters, including albumin(ALB), hemoglobin(HGB), blood urea nitrogen(BUN) and creatinine(CR). Fecal samples were collected before hospitalization and discharge, and stored at -80°C within 1 hour. And we assessed the microbial population and function by applying the 16S rRNA gene sequencing and functional enrichment analysis. RESULTS: Compared to control group, ALB is improved in both probiotics and FSG groups, while HGB is increased but BUN and CR is reduced in FSG group. Sequencing of 16S rRNA genes revealed that FSG and PRO affected the composition of the microbial community. FSG significantly increased a abundant represented by Bacteroides, Megamonas and Rothia, which was significantly correlated with the improvements in carbohydrate and amino acid metabolism. CONCLUSIONS: This study demonstrates that FSG ameliorates the nutritional status and improves the quality of life by enriching beneficial bacteria associated with metabolism. These results indicate that FSG as alternative medicine is a promising treatment for patients with PDRP.


Asunto(s)
Medicamentos Herbarios Chinos/farmacología , Microbioma Gastrointestinal/efectos de los fármacos , Diálisis Peritoneal/efectos adversos , Peritonitis/tratamiento farmacológico , Peritonitis/etiología , Anciano , Nitrógeno de la Urea Sanguínea , Heces/microbiología , Femenino , Microbioma Gastrointestinal/genética , Humanos , Masculino , Persona de Mediana Edad , Calidad de Vida , ARN Ribosómico 16S/análisis , Albúmina Sérica Humana/análisis , Resultado del Tratamiento
3.
Medicine (Baltimore) ; 100(16): e25623, 2021 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-33879734

RESUMEN

ABSTRACT: Microbiota has been suggested to play a role in patients with intestinal and cutaneous diseases. However, the profiling of perianal eczema microbiota has not been described. We have explored the general profile and possible differences between acute and chronic perianal eczema. A total of 101 acute perianal eczema (APE) and 156 chronic perianal eczema (CPE) patients were enrolled in this study and the perianal microbiota was profiled via Illumina sequencing of the 16S rRNA V4 region.The microbial α-diversity and structure are similar in APE and CPE patients; however, the perianal microbiota of the APE patients had a higher content of Staphylococcus (22.2%, P < .01) than that of CPE patients. Top10 genera accounting for more than 60% (68.81% for APE and 65.47% for CPE) of the whole microbiota, including Prevotella, Streptococcus, and Bifidobacterium, show an upregulation trend in the case of APE without reaching statistically significant differences. This study compared the microbiota profiles of acute and chronic perianal eczema. Our results suggest that the microbiota of acute perianal eczema patients is enriched in Staphylococcus compared with that in the chronic group. Our findings provide data for further studies.


Asunto(s)
Enfermedades del Ano/microbiología , Eccema/microbiología , Microbiota , Enfermedad Aguda , Adulto , Canal Anal/microbiología , Bifidobacterium/aislamiento & purificación , Enfermedad Crónica , Recuento de Colonia Microbiana , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , ARN Ribosómico 16S/análisis , Piel/microbiología , Staphylococcus/aislamiento & purificación , Streptococcus/aislamiento & purificación
4.
Biomed Res Int ; 2021: 6667623, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33763483

RESUMEN

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used in clinical microbiology laboratories because it is cost-effective, reliable, and fast. This study is aimed at comparing the identification performance of the recently developed Autof ms1000 (Autobio, China) with that of the Bruker Biotyper (Bruker Daltonics, Germany). From January to June 2020, 205 preserved strains and 302 clinical isolates were used for comparison. Bacteria were tested with duplicates of the direct transfer method, and formic acid extraction was performed if the results were not at the species level. Fungi were tested with formic acid extraction followed by ethanol extraction methods. 16S rRNA or ITS region sequence analysis was performed on isolates that could not be identified by any of the instruments and on isolates that showed inconsistent results. The time to result of each instrument was also compared. Among preserved strains, species-level identification results were obtained in 202 (98.5%) strains by the Autof ms1000 and 200 (97.6%) strains by the Bruker Biotyper. Correct identification at the species/complex level was obtained for 200 (97.6%) strains by the Autof ms1000 and for 199 (97.1%) strains by the Bruker Biotyper. Among clinical isolates, species-level identification results were obtained in 301 (99.7%) strains and 300 (99.3%) strains by the Autof ms1000 and Bruker Biotyper, respectively. Correct identification at the species/complex level was achieved for 299 (99.0%) strains by the Autof ms1000 and for 300 (99.3%) strains by the Bruker Biotyper. The time to analyze 96 spots was approximately 14 min for the Autof ms1000 and approximately 27 min for the Bruker Biotyper. The two instruments showed comparable performance for the routine identification of clinical microorganisms. In addition, the Autof ms1000 has a short test time, making it convenient for use in clinical microbiology laboratories.


Asunto(s)
Bacterias , Técnicas de Tipificación Bacteriana , ARN Bacteriano , ARN Ribosómico 16S , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Bacterias/clasificación , Bacterias/genética , Técnicas de Tipificación Bacteriana/instrumentación , Técnicas de Tipificación Bacteriana/métodos , Humanos , ARN Bacteriano/análisis , ARN Bacteriano/genética , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética
5.
Appl Environ Microbiol ; 87(11)2021 05 11.
Artículo en Inglés | MEDLINE | ID: mdl-33741635

RESUMEN

Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the food web and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, and some of these changes are repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every 2 weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses-the gene encoding the major capsid protein of T4-like phages and their relatives (gp23) and the RNA-dependent RNA polymerase (RdRp) gene of marnavirus-like RNA viruses-as well as marker genes for their bacterial and eukaryotic host communities, the genes encoding 16S rRNA and 18S rRNA. There were strong lagged correlations between viral diversity and community similarity of putative hosts, implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically related viruses shifted over time, and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage, the ephemeral and persistent taxa were closely related, implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages.IMPORTANCE Viruses are major agents of microbial mortality in marine systems, yet little is known about changes in the composition of viral assemblages in relation to those of the microbial communities that they infect. Here, we sampled coastal seawater every 2 weeks for 1 year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral assemblages is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes, the highly dynamic shuffling of viral genotypes occurs largely within a few subsets of related individuals.


Asunto(s)
Filogenia , Agua de Mar/virología , Virus/clasificación , Colombia Británica , ARN Ribosómico 16S/análisis , ARN Ribosómico 18S/análisis , ARN Viral/análisis , Virus/aislamiento & purificación
6.
ACS Nano ; 15(1): 1167-1178, 2021 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-33498106

RESUMEN

Existing methods for RNA diagnostics, such as reverse transcription PCR (RT-PCR), mainly rely on nucleic acid amplification (NAA) and RT processes, which are known to introduce substantial issues, including amplification bias, cross-contamination, and sample loss. To address these problems, we introduce a confinement effect-inspired Cas13a assay for single-molecule RNA diagnostics, eliminating the need for NAA and RT. This assay involves confining the RNA-triggered Cas13a catalysis system in cell-like-sized reactors to enhance local concentrations of target and reporter simultaneously, via droplet microfluidics. It achieves >10 000-fold enhancement in sensitivity when compared to the bulk Cas13a assay and enables absolute digital single-molecule RNA quantitation. We experimentally demonstrate its broad applicability for precisely counting microRNAs, 16S rRNAs, and SARS-CoV-2 RNA from synthetic sequences to clinical samples with excellent accuracy. Notably, this direct RNA diagnostic technology enables detecting a wide range of RNA molecules at the single-molecule level. Moreover, its simplicity, universality, and excellent quantification capability might render it to be a dominant rival to RT-qPCR.


Asunto(s)
Sistemas CRISPR-Cas , Microfluídica , ARN/análisis , Línea Celular Tumoral , Enterococcus faecalis , Escherichia coli , Humanos , Klebsiella pneumoniae , Células MCF-7 , MicroARNs/análisis , Pseudomonas aeruginosa , ARN Ribosómico 16S/análisis , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Staphylococcus aureus
7.
Food Chem ; 348: 129116, 2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-33508610

RESUMEN

ß-Glucan as a component of grain cell walls is consumed daily. However, little is known about whether ß-glucan is influenced by the gastrointestinal environment. In this study, we aim to investigate the integrated metabolic process of cereal ß-glucan. In vitro simulated digestion and fermentation combined with microbiome and metabolome analysis were used to profile the metabolism of ß-glucan. Intriguingly, we found that ß-glucan was not hydrolyzed by digestive enzymes but partially degraded by gastric acid environment during in vitro digestion. Moreover, ß-glucan was utilized by gut microbiota to produce acetate, propionate and butyrate, concurrently, the relative abundance of Lactobacillus significantly increased and Escherichia-Shigella significantly decreased. The correlation analysis between metabolomics datasets and microorganisms revealed that ß-glucan catabolism was also accompanied by amino acid catabolism and linoleic acid biosynthesis. Our study offered a forceful basis for the further exploration of the role of ß-glucan and gut microbiota in host health.


Asunto(s)
Avena/metabolismo , beta-Glucanos/metabolismo , Animales , Técnicas de Cultivo Celular por Lotes , Digestión , Análisis Discriminante , Ácido Gástrico/química , Microbioma Gastrointestinal/efectos de los fármacos , Hidrólisis , Lactobacillus/genética , Lactobacillus/crecimiento & desarrollo , Lactobacillus/metabolismo , Análisis de los Mínimos Cuadrados , Ratones , Ratones Endogámicos C57BL , Análisis de Componente Principal , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética , beta-Glucanos/química , beta-Glucanos/farmacología
8.
Food Chem ; 348: 129136, 2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-33516996

RESUMEN

Material identification in processed and unprocessed food and feed is crucial for ensuring the safety and hygiene of food and feed products. Therefore, to identify possible marine mammal components in feed, we study developed a DNA microarray with species-specific oligonucleotide probes that enable the rapid identification of five important marine mammal species (dolphins, seals, sea lions, white whales, and finless porpoises). The assay was tested using five target marine mammal species, and the probe patterns were compared with those of three fish meals (for feed) to see if they contained traces of marine mammals. All five marine mammal species could be distinguished by the microarray, and no marine mammal-derived ingredients were detected in the three fish meals. This study indicates that DNA microarray-based detection is relatively easy and effective for identification of non-compliant marine mammal ingredients in seafood or feed.


Asunto(s)
Alimentación Animal/análisis , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , ARN Ribosómico 16S/análisis , Animales , Delfines/fisiología , Peces/genética , Análisis de los Alimentos , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismo , Phocidae/fisiología , Ballenas/fisiología
9.
Appl Environ Microbiol ; 87(7)2021 03 11.
Artículo en Inglés | MEDLINE | ID: mdl-33452030

RESUMEN

Wastewater management in the Canadian Arctic is challenging due to climate extremes, small population sizes, and lack of conventional infrastructure for wastewater treatment. Although many northern communities use waste stabilization ponds (WSPs) as their primary form of wastewater treatment, few studies have explored WSP microbial communities and assessed effluent impacts on receiving waters from a microbiological perspective. Here, we used 16S rRNA gene and metagenome sequencing to characterize WSP and receiving water microbial communities for two time points bracketing the spring WSP thaw in Baker Lake (Nunavut) and compared these results to other Nunavut WSPs in Cambridge Bay and Kugluktuk. Most amplicon sequence variants (ASVs) recovered from these WSP samples belonged to the phylum Proteobacteria, with considerable variation between the three locations and only six ASVs shared among the WSPs at >0.2% relative abundance. Wastewater indicator ASVs for the Baker Lake WSP were identified, and few indicator ASVs were detected in samples originating from other upstream or downstream sites. The metagenomic data revealed a strong enrichment of antibiotic resistance genes for WSP samples relative to downstream and reference samples, especially for genes associated with macrolide resistance. Together, our results provide a baseline characterization for WSP microbial communities, demonstrate how indicator ASVs can be used to monitor attenuation and dilution of effluent microorganisms, and reveal that WSPs can serve as hot spots for antibiotic resistance genes.IMPORTANCE Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator amplicon sequence variants (ASVs) of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes. Given operational and infrastructure changes anticipated for wastewater treatment systems in the Arctic, baseline data such as these are essential for further development of safe and effective wastewater treatment systems.


Asunto(s)
Bacterias/genética , Farmacorresistencia Bacteriana/genética , Metagenoma , Eliminación de Residuos Líquidos , Aguas Residuales/microbiología , Bacterias/efectos de los fármacos , Microbiota , Nunavut , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Análisis de Secuencia de ARN
10.
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
11.
Appl Environ Microbiol ; 87(7)2021 03 11.
Artículo en Inglés | MEDLINE | ID: mdl-33483310

RESUMEN

Mucoromycota representatives are known to harbor two types of endohyphal bacteria (EHB)-Burkholderia-related endobacteria (BRE) and Mycoplasma-related endobacteria (MRE). While both BRE and MRE occur in fungi representing all subphyla of Mucoromycota, their distribution is not well studied. Therefore, it is difficult to resolve the evolutionary history of these associations in favor of one of the following two alternative hypotheses explaining their origin: "early invasion" and "late invasion." Our main goal was to fill this knowledge gap by surveying Mucoromycota fungi for the presence of EHB. We screened 196 fungal strains from 16 genera using a PCR-based approach to detect bacterial 16S rRNA genes, complemented with fluorescence in situ hybridization (FISH) imaging to confirm the presence of bacteria within the hyphae. We detected Burkholderiaceae in ca. 20% of fungal strains. Some of these bacteria clustered phylogenetically with previously described BRE clades, whereas others grouped with free-living Paraburkholderia Importantly, the latter were detected in Umbelopsidales, which previously were not known to harbor endobacteria. Our results suggest that this group of EHB is recruited from the environment, supporting the late invasion scenario. This pattern complements the early invasion scenario apparent in the BRE clade of EHB.IMPORTANCE Bacteria living within fungal hyphae present an example of one of the most intimate relationships between fungi and bacteria. Even though there are several well-described examples of such partnerships, their prevalence within the fungal kingdom remains unknown. Our study focused on early divergent terrestrial fungi in the phylum Mucoromycota. We found that ca. 20% of the strains tested harbored bacteria from the family Burkholderiaceae Not only did we confirm the presence of bacteria from previously described endosymbiont clades, we also identified a new group of endohyphal Burkholderiaceae representing the genus Paraburkholderia We established that more than half of the screened Umbelopsis strains were positive for bacteria from this new group. We also determined that, while previously described BRE codiverged with their fungal hosts, Paraburkholderia symbionts did not.


Asunto(s)
Burkholderiaceae/fisiología , Hongos/fisiología , Hifa/fisiología , Hibridación Fluorescente in Situ , Reacción en Cadena de la Polimerasa , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis
12.
J Vet Diagn Invest ; 33(2): 345-347, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33446090

RESUMEN

A 1-mo-old reticulated giraffe had progressive anorexia and died at the Ordos Zoo. Autopsy revealed necrotic stomatitis with severe bilateral necroulcerative lesions at the base of the tongue and of the cheeks near the commissures of the mouth. There was also severe bilateral confluent bronchopneumonia with a pronounced bronchial pattern and multifocal fibrinous pleuritis. Histologically, there was serofibrinous-suppurative bronchopneumonia with necrosuppurative bronchiolitis and necrotic arteritis. Filamentous bacteria with morphology consistent with Fusobacterium necrophorum were observed at the advancing edge of the necrotic tissue in the tongue and cheeks, as well as in the affected alveolar spaces and bronchioles. Aggregates of slender, gram-negative, rod-like or filamentous bacteria were identified in the lung impression smear. PCR results of 16S rDNA of the tongue and lung lesions had 100% homology to the F. necrophorum subsp. funduliforme B35 sequence (EF447425.1). The gross, histologic, Gram stain, and PCR product sequencing features in our case were consistent with oral and pulmonary necrobacillosis in ruminants, a rare disease of giraffes.


Asunto(s)
Infecciones por Fusobacterium/veterinaria , Fusobacterium necrophorum/aislamiento & purificación , Jirafas , Enfermedades Pulmonares/veterinaria , Enfermedades de la Boca/veterinaria , Animales , Animales de Zoológico , China , Infecciones por Fusobacterium/diagnóstico , Infecciones por Fusobacterium/microbiología , Fusobacterium necrophorum/genética , Pulmón/patología , Enfermedades Pulmonares/diagnóstico , Enfermedades Pulmonares/microbiología , Boca/patología , Enfermedades de la Boca/diagnóstico , Enfermedades de la Boca/microbiología , Reacción en Cadena de la Polimerasa/veterinaria , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis
13.
Trop Anim Health Prod ; 53(1): 50, 2020 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-33369699

RESUMEN

The aim of this study was to characterize the colostrum and fecal microbiota in calves and to investigate whether fecal microbiota composition was related to colostrum microbiota or factors associated with calf health. Colostrum samples were collected in buckets after hand milking of 76 calving cows from 38 smallholder dairy farms. Fecal samples were taken directly from the rectum of 76 calves at birth and at 14 days age. The bacterial community structure in colostrum and feces was analyzed by terminal restriction fragment length polymorphism for all samples, and the microbial composition was determined by 16S rRNA gene amplicon sequencing for a subset of the samples (8 colostrum, 40 fecal samples). There was a significant difference in fecal microbiota composition between day 0 and day 14 samples, but no associations between the microbiota and average daily gain, birth weight, or transfer of passive immunity. At 14 days of age, Faecalibacterium and Butyricicoccus were prevalent in higher relative abundances in the gut of healthy calves compared to calves with diarrhea that had been treated with antimicrobials. Colostrum showed great variation in composition of microbiota but no association to fecal microbiota. This study provides the first insights into the composition of colostrum and fecal microbiota of young dairy calves in southern Vietnam and can form the basis for future more detailed studies.


Asunto(s)
Bacterias/clasificación , Bovinos/microbiología , Calostro/microbiología , Heces/microbiología , Microbioma Gastrointestinal , Animales , Animales Recién Nacidos , Bacterias/aislamiento & purificación , Enfermedades de los Bovinos/microbiología , Diarrea/microbiología , Diarrea/veterinaria , Femenino , Masculino , Microbiota , Leche , Embarazo , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Vietnam
14.
Appl Environ Microbiol ; 86(23)2020 11 10.
Artículo en Inglés | MEDLINE | ID: mdl-32978127

RESUMEN

Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.


Asunto(s)
Archaea/aislamiento & purificación , Bacterias/aislamiento & purificación , Nitrógeno/metabolismo , Microbiología del Suelo , Archaea/genética , Bacterias/genética , Fertilizantes/análisis , Perfilación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , ARN de Archaea/análisis , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Reacción en Cadena en Tiempo Real de la Polimerasa , Transcripción Genética
15.
Appl Environ Microbiol ; 86(23)2020 11 10.
Artículo en Inglés | MEDLINE | ID: mdl-32978131

RESUMEN

The compositions of Octopus Spring and Mushroom Spring (Yellowstone National Park, Wyoming, USA) microbial mats have been thoroughly studied, but the compositions of the effluent waters that flow above the mats have not. In this study, cells in the mats and overflowing waters of both springs were investigated at multiple sites where Synechococcus spp. are the dominant cyanobacteria (ca. 72°C to ca. 50°C), and on several dates. In addition to microscopic analyses of stained and autofluorescent cells, 16S rRNA gene sequencing was used to characterize the major taxa present and a protein-encoding gene (psaA) was sequenced and analyzed by ecotype simulation to predict species of Synechococcus The mats of both springs were similar in terms of the downstream distribution of predominant taxa detected previously. However, waters above these mats were predominated by taxa that reside in upstream mats or communities above the upper-temperature limit of the mat. A disturbance/recolonization study was performed at a site normally predominated by Synechococcus species adapted to low temperatures. After removing indigenous Synechococcus cells, Synechococcus species adapted to higher temperatures, which were predominant in the water overflowing this site, colonized the newly forming mat. Differences in recolonization under reduced and UV-screened irradiance suggested that, in addition to physical transport, environmental conditions likely select for species that are better adapted to these different conditions and can influence mat recovery. A transport model was developed and used to predict that, in Mushroom Spring, erosion predominates in the narrower and deeper upstream effluents and deposition predominates over erosion in wider and shallower downstream effluents.IMPORTANCE In flowing aquatic systems, cell erosion and deposition are important to the dispersal of cells from one location to another. Very little is known about microbial dispersal and the physical processes that underlie it. This study demonstrates its importance to colonization of downstream surfaces and especially to the recolonization and functioning of disturbed sites. Ecological systems in flowing environments are often, roughly speaking, pseudosteady, in that nutrients enter the system and by-products leave at relatively steady rates. Over time, material inputs and outputs must balance. Measurements of input fluxes (e.g., growth rates and proxies, such as photosynthesis rates) are frequent. However, erosion and deposition of cells are seldom measured and ecological significance is sometimes neglected. The importance of these parameters is immediately evident in any attempt to construct a model of long-time community behavior, as spatial ecological structure is significantly impacted and can be dominated by migration of organisms, even in small numbers.


Asunto(s)
Bacterias/aislamiento & purificación , Manantiales de Aguas Termales/microbiología , Microbiota , Bacterias/clasificación , Proteínas Bacterianas/análisis , Concentración de Iones de Hidrógeno , Parques Recreativos , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Synechococcus/clasificación , Synechococcus/aislamiento & purificación , Wyoming
16.
Chemosphere ; 254: 126842, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32957273

RESUMEN

Diffusion, sorption-desorption, and biodegradation influence chlorinated solvent storage in, and release (mass flux) from, low-permeability media. Although bioenhanced dissolution of non-aqueous phase liquids has been well-documented, less attention has been directed towards biologically-mediated enhanced diffusion from low-permeability media. This process was investigated using a heterogeneous aquifer cell, packed with 20-30 mesh Ottawa sand and lenses of varying permeability (1.0 × 10-12-1.2 × 10-11 m2) and organic carbon (OC) content (<0.1%-2%), underlain by trichloroethene (TCE)-saturated clay. Initial contaminant loading was attained by flushing with 0.5 mM TCE. Total chlorinated ethenes removal by hydraulic flushing was then compared for abiotic and bioaugmented systems (KB-1® SIREM; Guelph, ON). A numerical model incorporating coupled diffusion and (de)sorption facilitated quantification of bio-enhanced TCE release from low-permeability lenses, which ranged from 6% to 53%. Although Dehalococcoides mccartyi (Dhc) 16S rRNA genes were uniformly distributed throughout the porous media, strain-specific distribution, as indicated by the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA, was influenced by physical and chemical heterogeneity. Cells harboring the bvcA gene comprised 44% of the total RDase genes in the lower clay layer and media surrounding high OC lenses, but only 2% of RDase genes at other locations. Conversely, cells harboring the vcrA gene comprised 50% of RDase genes in low-permeability media compared with 85% at other locations. These results demonstrate the influence of microbial processes on back diffusion, which was most evident in regions with pronounced contrasts in permeability and OC content. Bioenhanced mass transfer and changes in the relative abundance of Dhc strains are likely to impact bioremediation performance in heterogeneous systems.


Asunto(s)
Chloroflexi/metabolismo , Contaminantes Químicos del Agua/aislamiento & purificación , Adsorción , Biodegradación Ambiental , ADN Bacteriano/genética , Difusión , Agua Subterránea , Dinámica Poblacional , Porosidad , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética , Tricloroetileno/aislamiento & purificación , Tricloroetileno/metabolismo , Contaminantes Químicos del Agua/metabolismo
17.
Intern Med ; 59(17): 2089-2094, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32879200

RESUMEN

Objective The relationship between gut microbiota and portal hypertension remains unclear. We investigated the characteristics of the gut microbiota in portal hypertension patients with esophago-gastric varices and liver cirrhosis. Methods Thirty-six patients (12 patients with portal hypertension, 12 healthy controls, and 12 non-cirrhosis patients) were enrolled in this university hospital study. Intestinal bacteria and statistical analyses were performed up to the genus level using the terminal restriction fragment length polymorphism method targeting 16S ribosomal RNA genes, with diversified regions characterizing each bacterium. Results Levels of Lactobacillales were significantly higher (p=0.045) and those of Clostridium cluster IV significantly lower (p=0.014) in patients with portal hypertension than in other patients. This Clostridium cluster contains many butanoic acid-producing strains, including Ruminococcace and Faecalibacterium prausnitzii. Clostridium cluster IX levels were also significantly lower (p=0.045) in portal hypertension patients than in other patients. There are many strains of Clostridium that produce propionic acid, and the effects on the host and the function of these bacterial species in the human intestine remain unknown. Regarding the Bifidobacterium genus, which is supposed to decrease as a result of cirrhosis, no significant decrease was observed in this study. Conclusion In the present study, we provided information on the characteristics of the gut microbiota of portal hypertension patients with esophago-gastric varices due to liver cirrhosis. In the future, we aim to develop probiotic treatments following further analyses that include the species level, such as the intestinal flora analysis method and next-generation sequencers.


Asunto(s)
Bacterias/aislamiento & purificación , Microbioma Gastrointestinal , Hipertensión Portal/microbiología , Cirrosis Hepática/complicaciones , Adulto , Bacterias/genética , Bifidobacterium/aislamiento & purificación , Clostridium/aislamiento & purificación , Várices Esofágicas y Gástricas/etiología , Femenino , Humanos , Hipertensión Portal/etiología , Intestinos/microbiología , Masculino , Persona de Mediana Edad , Probióticos/uso terapéutico , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Streptococcus/aislamiento & purificación
18.
Medicine (Baltimore) ; 99(37): e21788, 2020 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-32925716

RESUMEN

Hepatocellular carcinoma (HCC) is one of the most common neoplasms encountered, and its incidence is increasing worldwide. In this study, we explored the characteristics of gut microbiota in patients with primary hepatocellular carcinoma in advanced stage who received immune checkpoint inhibitors (ICIs) based on a large population with hepatitis B virus infection. An initial cohort of 65 patients with metastatic melanoma were included in this study. All patients were treated with ICIs at Fujian provincial geriatric hospital between August 2016 and June 2018. The 16S rDNA V4 region was amplified by Polymerase chain reaction and sequenced on the MiSeq platform. We found that the diversities of the gut microbiota in HCC who received ICIs were obviously increased. Negative feedback, which is controlled by interplay between microbial metabolic activities and host pathways, is thought to promote high bacterial diversity. We focused on the Faecalibacterium genus in response group, and Bacteroidales order in non-response group, and stratified patients into high versus low categories based on the median relative abundance of these taxa in the gut microbiome. Patients with high Faecalibacterium abundance had a significantly prolonged PFS versus those with a low abundance. Conversely, patients with a high abundance of Bacteroidales had a shortened progressive free survival compared to those with a low abundance. In summary, the present study examined the oral and gut microbiome of HCC patients undergoing immune checkpoint inhibitors immunotherapy. Significant differences were observed in the diversity and composition of the patient gut microbiome of responders versus non-responders.


Asunto(s)
Carcinoma Hepatocelular/microbiología , Microbioma Gastrointestinal , Factores Inmunológicos/uso terapéutico , Inmunoterapia/mortalidad , Neoplasias Hepáticas/microbiología , Anciano , Bacteroides/crecimiento & desarrollo , Carcinoma Hepatocelular/tratamiento farmacológico , Carcinoma Hepatocelular/mortalidad , China , Faecalibacterium/crecimiento & desarrollo , Femenino , Humanos , Inmunoterapia/métodos , Neoplasias Hepáticas/tratamiento farmacológico , Neoplasias Hepáticas/mortalidad , Masculino , Persona de Mediana Edad , Supervivencia sin Progresión , Estudios Prospectivos , ARN Ribosómico 16S/análisis , Resultado del Tratamiento
19.
Phytomedicine ; 79: 153322, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32920286

RESUMEN

BACKGROUND: Gut-heart axis has emerged as a novel concept to provide new insights into the complex mechanisms of heart failure (HF) and offer new therapeutic targets. Cardiac hypertrophy (CH) is one of the etiological agents contributing to the development of HF. Baoyuan Decoction (BYD), a traditional Chinese medicine (TCM) formula, exhibits unambiguous effects on treating CH and preventing HF. Previously, we have reported that BYD-targeted endogenous metabolites are potentially linked to gut microbiota metabolism, but the contribution of gut microbiota and metabolic interaction to the cardioprotective efficacy of BYD remains to be elucidated. PURPOSE: To investigate whether the gut microbiota plays a key role in anti-CH effects of BYD. STUDY DESIGN: A comprehensive strategy via incorporating pharmacodynamics, microbiomics, metabolomics, and microflora suppression model was adopted to investigate the links between the microbiota-host metabolic interaction and BYD efficacy in CH rats. METHOD: Firstly, the efficacy evaluation of BYD in treating chronic isoproterenol (ISO)-induced CH rats was performed by using multiple pharmacodynamic approaches. Then, the fecal metabolomics and 16S rRNA sequencing techniques were used to obtain the microbial and metabolic features of BYD against CH. After that, the potential gut-heart axis-based mechanism of BYD against CH was predicted by bioinformatic network analysis and validated by multiple molecular biology approaches. Finally, the antibiotics (AB)-induced gut microbiota suppression was employed to investigate whether the anti-CH effects of BYD is associated with the gut microflora. RESULTS: The fecal microbial communities and metabolic compositions were significantly altered in ISO-induced CH rats, while BYD effectively ameliorated the CH-associated gut microbiota dysbiosis, especially of Firmicutes and Bacteroidetes, and time-dependently alleviated the disturbance of fecal metabolome and reversed the changes of key CH and gut microbiota-related metabolites, such as short/medium chain fatty acids, primary/secondary bile acids, and amino acids. The mechanism study showed that the anti-CH effect of BYD was related to inhibition of the derivatives of arginine and tryptophan and their downstream pro-hypertrophic, pro-inflammatory, and pro-oxidant signaling pathways. The following microflora suppression test showed that BYD-mediated myocardial protection was decreased either in pharmacodynamics or in metabolic modulation. CONCLUSION: This study demonstrates that the protection of BYD against CH is partially gut microbiota dependent, and the regulatory effects of gut metabolism-related tryptophan and arginine derivatives is an important cardioprotection mechanism of BYD.


Asunto(s)
Cardiomegalia/tratamiento farmacológico , Cardiomegalia/microbiología , Cardiotónicos/farmacología , Medicamentos Herbarios Chinos/farmacología , Microbioma Gastrointestinal/efectos de los fármacos , Animales , Cardiomegalia/patología , Disbiosis/tratamiento farmacológico , Disbiosis/etiología , Disbiosis/microbiología , Heces/química , Heces/microbiología , Microbioma Gastrointestinal/genética , Corazón/efectos de los fármacos , Isoproterenol/toxicidad , Masculino , Redes y Vías Metabólicas/efectos de los fármacos , Metaboloma/efectos de los fármacos , Miocardio/metabolismo , Miocardio/patología , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética , Ratas Sprague-Dawley
20.
Appl Environ Microbiol ; 86(23)2020 11 10.
Artículo en Inglés | MEDLINE | ID: mdl-32948523

RESUMEN

In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host's diet.IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.


Asunto(s)
Bacterias/aislamiento & purificación , Dieta/veterinaria , Heces/microbiología , Microbioma Gastrointestinal , Mamíferos/microbiología , Mamíferos/fisiología , Animales , Bacterias/clasificación , Perfilación de la Expresión Génica/veterinaria , Metagenómica , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Especificidad de la Especie
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