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1.
BMC Med ; 19(1): 37, 2021 02 11.
Artículo en Inglés | MEDLINE | ID: mdl-33568158

RESUMEN

BACKGROUND: Chronic inflammation, which can be modulated by diet, is linked to high white blood cell counts and correlates with higher cardiometabolic risk and risk of more severe infections, as in the case of COVID-19. METHODS: Here, we assessed the association between white blood cell profile (lymphocytes, basophils, eosinophils, neutrophils, monocytes and total white blood cells) as markers of chronic inflammation, habitual diet and gut microbiome composition (determined by sequencing of the 16S RNA) in 986 healthy individuals from the PREDICT-1 nutritional intervention study. We then investigated whether the gut microbiome mediates part of the benefits of vegetable intake on lymphocyte counts. RESULTS: Higher levels of white blood cells, lymphocytes and basophils were all significantly correlated with lower habitual intake of vegetables, with vegetable intake explaining between 3.59 and 6.58% of variation in white blood cells after adjusting for covariates and multiple testing using false discovery rate (q < 0.1). No such association was seen with fruit intake. A mediation analysis found that 20.00% of the effect of vegetable intake on lymphocyte counts was mediated by one bacterial genus, Collinsella, known to increase with the intake of processed foods and previously associated with fatty liver disease. We further correlated white blood cells to other inflammatory markers including IL6 and GlycA, fasting and post-prandial glucose levels and found a significant relationship between inflammation and diet. CONCLUSION: A habitual diet high in vegetables, but not fruits, is linked to a lower inflammatory profile for white blood cells, and a fifth of the effect is mediated by the genus Collinsella. TRIAL REGISTRATION: The ClinicalTrials.gov registration identifier is NCT03479866 .


Asunto(s)
Dieta , Frutas , Microbioma Gastrointestinal/genética , Leucocitos , Verduras , Actinobacteria , Adulto , Biomarcadores/sangre , Clostridiales , Clostridium , Ayuno , Femenino , Humanos , Interleucina-6/sangre , Recuento de Leucocitos , Recuento de Linfocitos , Masculino , Persona de Mediana Edad , ARN Ribosómico 16S/genética , Ruminococcus
2.
Rev Soc Bras Med Trop ; 54: e05992020, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33533819

RESUMEN

INTRODUCTION: This study aimed to determine the role of genes encoding aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methylase (ArmA) in Acinetobacter baumannii clinical isolates. METHODS: We collected 100 clinical isolates of A. baumannii and identified and confirmed them using microbiological tests and assessment of the OXA-51 gene. Antibiotic susceptibility testing was carried out using disk agar diffusion and micro-broth dilution methods. The presence of AME genes and ArmA was detected by PCR and multiplex PCR. RESULTS: The most and least effective antibiotics in this study were netilmicin and ciprofloxacin with 68% and 100% resistance rates, respectively. According to the minimum inhibitory concentration test, 94% of the isolates were resistant to gentamicin, tobramycin, and streptomycin, while the highest susceptibility (20%) was observed against netilmicin. The proportion of strains harboring the aminoglycoside resistance genes was as follows: APH(3')-VIa (aphA6) (77%), ANT(2")-Ia (aadB) (73%), ANT(3")-Ia (aadA1) (33%), AAC(6')-Ib (aacA4) (33%), ArmA (22%), and AAC(3)-IIa (aacC2) (19%). Among the 22 gene profiles detected in this study, the most prevalent profiles included APH(3')-VIa + ANT(2")-Ia (39 isolates, 100% of which were kanamycin-resistant), and AAC(3)-IIa + AAC(6')-Ib + ANT(3")-Ia + APH(3')-VIa + ANT(2")-Ia (14 isolates, all of which were resistant to gentamicin, kanamycin, and streptomycin). CONCLUSIONS: High minimum inhibitory concentration of aminoglycosides in isolates with the simultaneous presence of AME- and ArmA-encoding genes indicated the importance of these genes in resistance to aminoglycosides. However, control of their spread could be effective in the treatment of infections caused by A. baumannii.


Asunto(s)
Acinetobacter baumannii , Acinetobacter baumannii/genética , Aminoglicósidos/farmacología , Antibacterianos/farmacología , Proteínas Bacterianas , Farmacorresistencia Bacteriana/genética , Metiltransferasas , Pruebas de Sensibilidad Microbiana , ARN Ribosómico 16S/genética
3.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 33(1): 10-16, 2021 Jan.
Artículo en Chino | MEDLINE | ID: mdl-33565393

RESUMEN

OBJECTIVE: To investigate the dynamic changes of intestinal flora in septic model mice. METHODS: Forty-two male SPF C57BL/6 mice were selected, the sepsis model was reproduced by cecal ligation and puncture (CLP), and the experimental mice were divided into CLP 6-12 hours group (n = 9) and 1, 2, 3 days group (all n = 10) and Sham group (n = 3) according to the time points after modeling. Intestinal flora 16S rRNA sequencing was carried out within feces from the colonic lumen of mice, and the effective sequences were clustered to obtain an operational classification unit (OTU) for statistical analysis of biological information, including Alpha diversity analysis, species composition analysis, principal coordinate analysis (PCoA analysis) and species difference analysis (LEfSe analysis), the dynamic changes of intestinal flora after CLP modeling were analyzed. RESULTS: Compared with Sham group, with the prolongation of modeling time, the Alpha diversity of intestinal flora decreased, showing a decrease in community richness index (3 days after CLP: Chao index 1 was 367.9±162.6 vs. 508.3±105.9, Ace index was 372.5±151.9 vs. 498.8±104.2), Shannon index decreased in community diversity index (3 days after CLP: 2.57±1.06 vs. 4.30±0.57, Simpson index increased (3 days after CLP: 0.26±0.19 vs. 0.04±0.03), suggesting that with the progress of CLP modeling time, the richness and diversity of intestinal flora decreased. According to species composition analysis, in OTU level, OTU 633 accounted for the highest proportion in CLP 1 day group (24.79%), OTU 1016 was dominant in CLP 2 days and 3 days groups, and the highest proportion was 61.75% in CLP 3 days group; in genus level, the abundance of norank_f_Muribaculaceae showed a slight increase and then a significant decrease with time, the abundance of Escherichia-Shigella increased significantly in CLP 2 days and 3 days groups, the abundance of Lactobacillus increased first and then decreased with time, the abundance of Bacteroides showed a trend of gradual increase with time. PCoA analysis suggested that CLP 6-12 hours group had a higher structural similarity with Sham group. The flora structure changed gradually with the time after modeling, and the change was significant after 3 days of CLP. LEfSe analysis indicated that the main components that caused the differences among the groups were g_norank_f_Muribaculaceae, g_Prevotellaceae_UCG-001, s_uncultured_Bacteroidales_bacterium_g_norank_f_Muribaculaceae, g_Parabacteroides, Escherichia-Shigella and OTU 1016. The differences in abundance of Escherichia-Shigella and OTU 016 among the five groups ranked first in the genus level and OTU level respectively; the abundance of Escherichia-Shigella gradually increased from 0.01% (0%, 0.02%) in 6-12 hours after CLP to 44.79% (3.71%, 53.75%) in 3 days with time, and the abundance of OTU 1016 increased from 0.01% (0%, 0.02%) in 6-12 hours after CLP to 44.69% (3.66%, 53.64%) in 3 days with time. CONCLUSIONS: Intestinal dysbiosis occurred in all CLP model groups, the diversity of the flora gradually decreased with the progress of modeling time, Escherichia-Shigella gradually became the dominant bacteria.


Asunto(s)
Microbioma Gastrointestinal , Sepsis , Animales , Disbiosis , Masculino , Ratones , Ratones Endogámicos C57BL , ARN Ribosómico 16S/genética
4.
Sci Total Environ ; 766: 144389, 2021 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-33429300

RESUMEN

A culture-independent DNA metabarcoding analysis of the bacterial communities was carried out throughout a complete vermicomposting cycle of municipal solid waste material using the earthworm Eisenia fetida. 16S rRNA amplicons from the initial material (0 days), an intermediate (42 days), and a final stage (84 days) were sequenced in an Illumina NGS platform and compared. A steady increase in community diversity was observed corresponding to a 2.5-fold higher taxa richness and correspondingly risen values of the Shannon and Simpson ecological indexes and the evenness parameter. A total of 49,665 operational taxonomic units (OTUs) were counted. From the qualitative standpoint, a clear successional shift was observed with an initial community dominated by putatively plant-associated groups belonging to the Rhizobiales order within the Alphaproteobacteria class, regressively leaving the scores of relative abundance (RA) to the Firmicutes phylum and in particular to the Bacilli. Vermistabilization of municipal solid waste (MSW) increased (p < 0.001) the TKN and total P content in the final vermicompost, while pH, TOC, and C/N ratio declined (p < 0.001) in the process. Likewise, a progressive decrease was noticed in ß-glucosidase, acid phosphatase, and urease activity while protease and dehydrogenase showed a slight increase, followed by a steep fall. A strong positive correlation was observed among the canonical functions of physico-chemical attributes and enzyme activities. The canonical correspondence analysis (CCA) revealed that significant families did not change on the temporal scale; however, their abundance was influenced by the abiotic environmental factors. In comparison to prior studies on vermicomposting that used different earthworm species (Eisenia andrei) and different substrates, results reflect a considerable degree of substrate specificity for the earthworm species used. The results offer clues to optimize the vermistabilization of MSW along with its potential use in agriculture, to foster improved levels of the circular economy.


Asunto(s)
Oligoquetos , Animales , Bacterias/genética , ARN Ribosómico 16S/genética , Suelo , Residuos Sólidos
5.
Artículo en Inglés | MEDLINE | ID: mdl-33464198

RESUMEN

Three Gram-stain-negative, rod-shaped, non-spore-forming bacteria, BA1T, Q614T and PB68.1T, isolated from the digestive system of Heterorhabditis entomopathogenic nematodes, were biochemically and molecularly characterized to clarify their taxonomic affiliations. The 16S rRNA gene sequences of these strains suggest that they belong to the Gammaproteobacteria, to the family Morganellacea, and to the genus Photorhabdus. Deeper analyses using whole genome-based phylogenetic reconstructions suggest that BA1T is closely related to Photorhabdus akhursti, that Q614T is closely related to Photorhabdus heterorhabditis, and that PB68.1T is closely related to Photorhabdus australis. In silico genomic comparisons confirm these observations: BA1T and P. akhursti 15138T share 68.8 % digital DNA-DNA hybridization (dDDH), Q614T and P. heterorhabditis SF41T share 75.4 % dDDH, and PB68.1T and P. australis DSM 17609T share 76.6  % dDDH. Physiological and biochemical characterizations reveal that these three strains also differ from all validly described Photorhabdus species and from their more closely related taxa, contrary to what was previously suggested. We therefore propose to classify BA1T as a new species within the genus Photorhabdus, Q614T as a new subspecies within P. heterorhabditis, and PB68.1T as a new subspecies within P. australis. Hence, the following names are proposed for these strains: Photorhabdus aegyptia sp. nov. with the type strain BA1T(=DSM 111180T=CCOS 1943T=LMG 31957T), Photorhabdus heterorhabditis subsp. aluminescens subsp. nov. with the type strain Q614T (=DSM 111144T=CCOS 1944T=LMG 31959T) and Photorhabdus australis subsp. thailandensis subsp. nov. with the type strain PB68.1T (=DSM 111145T=CCOS 1942T). These propositions automatically create Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov. with SF41T as the type strain (currently classified as P. heterorhabditis) and Photorhabdus australis subsp. australis subsp. nov. with DSM17609T as the type strain (currently classified as P. australis).


Asunto(s)
Nematodos/microbiología , Photorhabdus/clasificación , Filogenia , Animales , Australia , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Sistema Digestivo/microbiología , Egipto , Hibridación de Ácido Nucleico , Photorhabdus/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Tailandia
6.
Artículo en Inglés | MEDLINE | ID: mdl-33464199

RESUMEN

Wheat blue dwarf (WBD) is one of the most economically damaging cereal crop diseases in northwestern PR China. The agent associated with the WBD disease is a phytoplasma affiliated with the aster yellows (AY) group, subgroup C (16SrI-C). Since phytoplasma strains within the AY group are ecologically and genetically diverse, it has been conceived that the AY phytoplasma group may consist of more than one species. This communication presents evidence to demonstrate that, while each of the two 16 rRNA genes of the WBD phytoplasma shares >97.5 % sequence similarity with that of the 'Candidatus Phytoplasma asteris' reference strain, the WBD phytoplasma clearly represents an ecologically separated lineage: the WBD phytoplasma not only has its unique transmitting vector (Psammotettix striatus) but also elicits a distinctive symptom in its predominant plant host (wheat). In addition, the WBD phytoplasma possesses molecular characteristics that further manifest its significant divergence from 'Ca. P. asteris'. Such molecular characteristics include lineage-specific antigenic membrane proteins and a lower than 95 % genome-wide average nucleotide identity score with 'Ca. P. asteris'. These ecological, molecular and genomic evidences justify the recognition of the WBD phytoplasma as a novel taxon, 'Candidatus Phytoplasma tritici'.


Asunto(s)
Filogenia , Phytoplasma/clasificación , Enfermedades de las Plantas/microbiología , Triticum/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , China , ADN Bacteriano/genética , Phytoplasma/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
7.
BMC Surg ; 21(1): 28, 2021 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-33413260

RESUMEN

BACKGROUND: Managing surgical site infections, with negative culture report in routine diagnosis is a common dilemma in microbiology accounting more than 30% worldwide. The present study attempted to identify the presence of bacterial spp. if any in wound aspirates/swabs of culture negative surgical site infections of hospitalised patients using molecular tools. METHODS: Ninety-seven patients with post-operative SSI whose wound swabs/aspirate were negative in the conventional aerobic culture after 72 h of incubation were analysed by 16S rRNA gene specific broad range PCR. The amplified DNA fragments were sequenced by Sanger DNA sequencing method and homology of the sequence were matched using NCBI BLAST (NCBI, USA) RESULTS: Of the 97 patients, 16S rRNA based broad range PCR assay could identify the presence of bacterial pathogen in 53(54.63%) cases, of which 29 isolates were supposed to be of viable but non-culturable bacteria (VBNC), 07 were of obligatory anaerobes and 13 were of unculturable bacteria, 04 were with poly bacterial infections. CONCLUSIONS: Our study highlights the usefulness of PCR assay in detecting the presence of any VBNC, anaerobes and unculturable bacteria in SSI patients regardless of how well the bacteria may or may not grow in culture. Measures should be taken to use anaerobic culture system and PCR diagnosis along with conventional culture to detect the VBNC and unculturable bacteria where Gram stain is positive for better patient care.


Asunto(s)
Bacterias/genética , ADN Bacteriano/genética , ARN Ribosómico 16S/genética , Infección de la Herida Quirúrgica/microbiología , Humanos , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Infección de la Herida Quirúrgica/diagnóstico , Infección de la Herida Quirúrgica/epidemiología
8.
Sci Total Environ ; 763: 144119, 2021 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-33418471

RESUMEN

It is important that environmental parameters that may affect the prevalence of AmpC beta-lactamase genes are investigated to devise frameworks for their surveillance, management and prevention. The aim of this study was thus to determine which environmental parameters are associated with the prevalence of clinically relevant AmpC beta-lactamase genes in aquatic systems. River water was sampled from seven sites in the Crocodile West River, South Africa. Physical-chemical parameters, metal levels and beta-lactam levels were measured. Environmental DNA was extracted from the water samples and six AmpC beta-lactamase gene groups (ACC, ACT/MIR, BIL/LAT/CMY, DHA, FOX, MOX/CMY) were quantified using quantitative PCR. Additionally, 16S rRNA gene metabarcoding analyses were performed on eDNA for each site and metabolic pathways were predicted using PICRUST2. Network analysis was performed to establish co-occurrences of AmpC genes with environmental factors. Quantification results indicated that AmpC gene copy numbers were significantly high (Kruskal Wallis H Test, p < 0.05) at Sites 1-3 of the Crocodile West River. In contrast, no significant changes regarding environmental factors were observed across the seven sites. Results of network analysis indicated that the AmpC gene groups had limited associations with all the environmental parameters, except for some key bacterial families, specifically Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. A significant positive correlation between population density and AmpC genes suggested that in more densely populated areas more faecal pollution will be prevalent which is associated with high AmpC gene levels. Areas such as these are also likely to be linked with more antibiotic use which supports the notion that pre-selection of AmpC genes occurs before entering the aquatic environment. Moreover, it was demonstrated that prevalent selectors of AmpC genes do not ensure that continuous selection occurs in an aquatic environment. This information could be vital in future detection and management of AmpC genes in aquatic systems.


Asunto(s)
Proteínas Bacterianas , beta-Lactamasas , Antibacterianos , Proteínas Bacterianas/genética , Humanos , Pruebas de Sensibilidad Microbiana , Plásmidos , Prevalencia , ARN Ribosómico 16S/genética , Sudáfrica , beta-Lactamasas/genética
9.
Nat Commun ; 12(1): 161, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33420064

RESUMEN

Calf diarrhea is associated with enteric infections, and also provokes the overuse of antibiotics. Therefore, proper treatment of diarrhea represents a therapeutic challenge in livestock production and public health concerns. Here, we describe the ability of a fecal microbiota transplantation (FMT), to ameliorate diarrhea and restore gut microbial composition in 57 growing calves. We conduct multi-omics analysis of 450 longitudinally collected fecal samples and find that FMT-induced alterations in the gut microbiota (an increase in the family Porphyromonadaceae) and metabolomic profile (a reduction in fecal amino acid concentration) strongly correlate with the remission of diarrhea. During the continuous follow-up study over 24 months, we find that FMT improves the growth performance of the cattle. This first FMT trial in ruminants suggest that FMT is capable of ameliorating diarrhea in pre-weaning calves with alterations in their gut microbiota, and that FMT may have a potential role in the improvement of growth performance.


Asunto(s)
Enfermedades de los Bovinos/terapia , Bovinos/crecimiento & desarrollo , Diarrea/terapia , Trasplante de Microbiota Fecal/veterinaria , Microbioma Gastrointestinal/genética , Animales , Bacteroidaceae/genética , Bacteroidaceae/aislamiento & purificación , Bovinos/microbiología , Enfermedades de los Bovinos/sangre , Enfermedades de los Bovinos/metabolismo , Enfermedades de los Bovinos/microbiología , ADN Bacteriano/aislamiento & purificación , Diarrea/sangre , Diarrea/metabolismo , Diarrea/microbiología , Heces/microbiología , Femenino , Estudios de Seguimiento , Genómica , Masculino , Metabolómica , ARN Ribosómico 16S/genética , Resultado del Tratamiento
10.
Chemosphere ; 268: 129362, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33385834

RESUMEN

This study investigated the effects of accidental contamination of soils with phenol, toluene, nitric acid, and hydrogen fluoride (HF) by simulating chemical leakage in the soil with/without rain and characterizing the resulting metabolites and microbial. In the case of acid leakage, pH and cation exchange capacity were decreased, and the content of fluoride ion was increased in case of HF leakage. Using mass spectrometry-based metabolomics analysis, phytosphingosine was detected as a distinguishing metabolite in soils contaminated with phenol and HF in rain conditions. Microbial communities were identified by 16s rRNA metagenome sequencing. Sphingomonas was one of the dominant species in soils contaminated with phenol and HF. These results suggest that phytosphingosine and Sphingomonas might be used as biomarkers to evaluate the status of soils contaminated with phenol or HF. Under simulated rain conditions, the species alpha-diversity index of soil microbes and the physicochemical properties of the soil indicated values close to those of the uncontaminated soil. Rain played an important role in the recovery of microbial and metabolic profiles after chemical accidents. Metabolic profiling and microbial community analysis can serve as a diagnostic tool for ecotoxicological research at chemical accident sites.


Asunto(s)
Liberación de Peligros Químicos , Microbiota , Contaminantes del Suelo , Metabolómica , ARN Ribosómico 16S/genética , Suelo , Microbiología del Suelo , Contaminantes del Suelo/análisis , Contaminantes del Suelo/toxicidad
11.
Ecotoxicol Environ Saf ; 211: 111955, 2021 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-33497859

RESUMEN

Anthropogenic activities especially water pollution can affect the diversity and composition of microbial communities and promote the spread of antibiotic resistance genes (ARGs). In this study, water samples and guppies (Poecilia reticulata) were sampled from six sampling sites along the Uberabinha River in southeastern Brazil, both microbial communities and ARGs of surface waters and intestinal microbiota of guppies (Poecilia reticulata) were detected. According to the results of 16S rRNA amplicon sequencing, Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria were dominant phyla in both water and intestinal microbiota, but the abundance of putative pathogens was higher at heavily polluted sites. Up to 83% of bacteria in intestinal microbiota originated from water microbiota; this proportion was relatively higher in less polluted compared to polluted environments. ARGs providing resistance of tetracyclines and quinolones were dominant in both water and gut microbiota. The relative abundances of class I integrons and ARGs were as high as 1.74 × 10-1/16S rRNA copies and 3.61 × 10-1/16S rRNA copies, respectively, at heavily polluted sites. Correlation analysis suggests that integrons and bacteria play key roles in explaining the widespread occurrence of ARGs in the surface, but not in intestinal microbiota. We could rule out the class I integrons a potential intermediary bridge for ARGs between both types of microbiomes. Our results highlight the tight link in microbial communities and ARGs between ambient microbiota of stream ecosystems and intestinal microbiota of fish. Our study could have far-reaching consequences for fisheries and consumer safety and calls for investigations of gut microbiota of target species of both commercial fisheries and recreational (hobby) angling.


Asunto(s)
Farmacorresistencia Microbiana/genética , Microbioma Gastrointestinal/efectos de los fármacos , Genes Bacterianos , Poecilia/fisiología , Contaminación del Agua/estadística & datos numéricos , Animales , Antibacterianos/análisis , Bacterias/genética , Brasil , Integrones , Microbiota/genética , Poecilia/genética , Poecilia/microbiología , Quinolonas/análisis , ARN Ribosómico 16S/genética , Ríos/microbiología , Agua/análisis , Contaminación del Agua/análisis
12.
mBio ; 12(1)2021 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-33402535

RESUMEN

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.IMPORTANCE Our study reveals the ecogenomic traits of microorganisms participating in the cellulose economy of soil. We identified three major categories of participants in this economy: (i) independent primary degraders, (ii) interdependent primary degraders, and (iii) secondary consumers (mutualists, opportunists, and parasites). Trade-offs between independent primary degraders, whose adaptations favor antagonism and competitive exclusion, and interdependent and secondary degraders, whose adaptations favor complex interspecies interactions, are expected to affect the fate of microbially processed carbon in soil. Our findings provide useful insights into the ecological relationships that govern one of the planet's most abundant resources of organic carbon. Furthermore, we demonstrate a novel gradient-resolved approach for stable isotope probing, which provides a cultivation-independent, genome-centric perspective into soil microbial processes.


Asunto(s)
Agricultura , Celulosa/metabolismo , Metagenoma , Microbiología del Suelo , Suelo/química , Actinobacteria/genética , Actinobacteria/metabolismo , Actinomycetales/genética , Actinomycetales/metabolismo , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Biomasa , Caulobacteraceae/genética , Caulobacteraceae/metabolismo , Celulosa/química , Chaetomium/genética , Chaetomium/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Metagenómica , Filogenia , Proteobacteria/genética , Proteobacteria/metabolismo , ARN Ribosómico 16S/genética , Simbiosis
13.
Bioresour Technol ; 324: 124681, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33454444

RESUMEN

This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.


Asunto(s)
Microbiota , Aguas Residuales , Acidobacteria , Bacterias/genética , ARN Ribosómico 16S/genética
14.
Environ Monit Assess ; 193(1): 27, 2021 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-33389180

RESUMEN

Anthropogenic activities release effluents containing nutrients and pathogenic bacteria that change the characteristics of coastal ecosystems. An important type of marine pollution which has occurred in 3 different states in India during 2019 is sea foam. Sea foam was found on Hole beach, Goa (Lat: 15.404° N, Long: 73.787° E), where nutrients (NO3- = 137 µM and organic nitrogen = 121 µM) from a garbage dumpyard are released directly via streams/gutters to coastal waters. This resulted in a bloom of the diatom Thalassiosira pseudonana, associated with high concentration of total organic carbon and fucoxanthin. Decay of this bloom along with strong agitation due to rocks and wave action resulted in sea foam. We isolated foam-associated bacteria and identified pathogenic bacteria including Enterobacter cancerogenus through 16S rRNA gene sequencing. Such foam-associated pathogenic bacteria, could be antibiotic resistant, and may have adverse effects on human health. This can also hamper the tourism industry of a small state like Goa that relies heavily on tourism.


Asunto(s)
Ecosistema , Monitoreo del Ambiente , Enterobacter , Humanos , India , ARN Ribosómico 16S/genética
15.
Extremophiles ; 25(1): 85-99, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33416983

RESUMEN

Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microorganisms to early planet life conditions. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in Costa Rica. Both locations hold a low pH (1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO42- = 1170-2460 mg/L), but significant differences in their temperature (90.0-95.0 ºC in the seepages at Poas Volcano, 19.1-26.6 ºC in Agrio River) and in the elemental sulfur content. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp. represented more than half of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by Leptospirillum and members of the archaeal order Thermoplasmatales. Both environments share some chemical characteristics and part of their microbiota, however, the temperature and the reduced sulfur are likely the main distinguishing features, ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.


Asunto(s)
Calor , Microbiota , Filogenia , Azufre , Ácidos , Archaea/clasificación , Bacterias/clasificación , Costa Rica , Concentración de Iones de Hidrógeno , ARN Ribosómico 16S/genética , Ríos , Erupciones Volcánicas
16.
Environ Monit Assess ; 193(2): 56, 2021 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-33432373

RESUMEN

In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Community metagenomics revealed a total of 631 genera belonging to 22 different phyla, dominated by Proteobacteria (118,222 features), Firmicutes (101,043 features), Actinobacteria (34,189 features), Bacteroidetes (17,977 features), and Cyanobacteria (2730 features). The bacterial community identified was composed of both pathogenic zoonotic and non-harmful groups. The pathway or functional analysis of the fish gill microbiome exhibited 21 different pathways which also included the pathogenic-related functions. Our data detected a wide group of bacterial communities that will be useful in further isolating and characterizing the pathogenic bacteria from the fish and also to understand the bacterial association in highly consumed fish.


Asunto(s)
Microbiota , Ríos , Animales , Biodiversidad , Monitoreo del Ambiente , Branquias , India , ARN Ribosómico 16S/genética
17.
Arch Oral Biol ; 122: 105036, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33421657

RESUMEN

OBJECTIVE: This study aimed to investigate abundance of specific bacterial taxa in the saliva of 105 Thai adults with different BMI (lean, overweight, and obese) and T2DM subjects using qPCR targeting the 16S rRNA gene of various bacteria taxa. DESIGN: We employed qPCR targeting 16S rRNA genes to explore the bacterial profiles and abundances in the saliva of Thai adult subjects with different BMI and T2DM. Multivariate statistical analyses (multiple factor analysis (MFA) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) were performed to assess the associations of salivary bacteria with diet, blood profile, gender, age, and use of antibiotics. RESULTS: We found that abundance profiles of the examined salivary bacteria were similar across the four groups. When diet, blood profile, and gender, age, and use of antibiotics were considered, significant differences were noted between subgroups. A positive correlation was also found between consumption of carbonate soft drinks and Bacteroidetes, Gamma-proteobacteria, Veillonella, Fusobacterium and Fusobacterium nucleatum. CONCLUSIONS: This is the first study demonstrating the relative abundance of salivary bacteria in adult Thai subjects with different levels of BMI and T2DM. Regardless of the similar pattern of bacterial profiles across groups, sPLS-DA analysis highlighted the influence of host variables (gender, age, and use of antibiotics) on the abundance of salivary microbiota. Our findings pave the way for further hypothesis testing to gain insight into the association between host factors and salivary microbiome.


Asunto(s)
Dieta , Enfermedades Metabólicas/microbiología , Microbiota , Saliva/microbiología , Adulto , Bacterias/clasificación , Índice de Masa Corporal , Humanos , ARN Ribosómico 16S/genética , Tailandia
18.
J Anim Sci ; 99(1)2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-33515482

RESUMEN

The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split-plot design run as a crossover in two periods. The whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for the amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. The main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, and all possible interactions and random effect of horse. Alpha and beta diversities were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05), whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total VFA concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared with cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared with the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared with cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.


Asunto(s)
Alimentación Animal , Microbiota , Alimentación Animal/análisis , Animales , Ciego/metabolismo , Dieta/veterinaria , Heces , Fermentación , Caballos , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismo
19.
Water Res ; 192: 116852, 2021 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-33517045

RESUMEN

Plastic pollution in aquatic environments, particularly microplastics (<5 mm), is an emerging health threat. The buoyancy, hydrophobic hard surfaces, novel polymer carbon sources and long-distance transport make microplastics a unique substrate for biofilms, potentially harbouring pathogens and enabling antimicrobial resistance (AMR) gene exchange. Microplastic concentrations, their polymer types and the associated microbial communities were determined in paired, contemporaneous samples from the Dutch portion of the river Rhine. Microplastics were collected through a cascade of 500/100/10 µm sieves; filtrates and surface water were also analysed. Microplastics were characterized with infrared spectroscopy. Microbial communities and selected virulence and AMR genes were determined with 16S rRNA-sequencing and qPCR. Average microplastic concentration was 213,147 particles/m3; polyamide and polyvinylchloride were the most abundant polymers. Microbial composition on 100-500 µm samples differed significantly from surface water and 10-100 µm or smaller samples, with lower microbial diversity compared to surface water. An increasingly 'water-like' microbial community was observed as particles became smaller. Associations amongst specific microbial taxa, polymer types and particle sizes, as well as seasonal and methodological effects, were also observed. Known biofilm-forming and plastic-degrading taxa (e.g. Pseudomonas) and taxa harbouring potential pathogens (Pseudomonas, Acinetobacter, Arcobacter) were enriched in certain sample types, and other risk-conferring signatures like the sul1 and erm(B) AMR genes were almost ubiquitous. Results were generally compatible with the existence of taxon-selecting mechanisms and reduced microbial diversity in the biofilms of plastic substrates, varying over seasons, polymer types and particle sizes. This study provided updated field data and insights on microplastic pollution in a major riverine environment.


Asunto(s)
Microbiota , Contaminantes Químicos del Agua , Monitoreo del Ambiente , Microplásticos , Países Bajos , Plásticos , ARN Ribosómico 16S/genética , Contaminantes Químicos del Agua/análisis
20.
Water Res ; 191: 116779, 2021 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-33401166

RESUMEN

Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.


Asunto(s)
Aguas del Alcantarillado , Purificación del Agua , Anaerobiosis , Reactores Biológicos , Humanos , Hibridación Fluorescente in Situ , ARN Ribosómico 16S/genética
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