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1.
Int J Food Microbiol ; 328: 108668, 2020 Sep 02.
Artículo en Inglés | MEDLINE | ID: mdl-32474228

RESUMEN

Biofilms are comprised of microorganisms embedded in a self-produced matrix that normally adhere to a surface. In the food processing environment they are suggested to be a source of contamination leading to food spoilage or the transmission of food-borne pathogens. To date, research has mainly focused on the presence of (biofilm-forming) bacteria within food processing environments, without measuring the associated biofilm matrix components. Here, we assessed the presence of biofilms within a meat processing environment, processing pork, poultry and beef, by the detection of microorganisms and at least two biofilm matrix components. Sampling included 47 food contact surfaces and 61 non-food contact surfaces from eleven rooms within an Austrian meat processing plant, either during operation or after cleaning and disinfection. The 108 samples were analysed for the presence of microorganisms by cultivation and targeted quantitative real-time PCR based on 16S rRNA. Furthermore, the presence of the major matrix components carbohydrates, extracellular DNA and proteins was evaluated. Overall, we identified ten biofilm hotspots, among them seven of which were sampled during operation and three after cleaning and disinfection. Five biofilms were detected on food contact surfaces (cutters and associated equipment and a screw conveyor) and five on non-food contact surfaces (drains and water hoses) resulting in 9.3 % of the sites being classified as biofilm positive. From these biofilm positive samples, we cultivated bacteria of 29 different genera. The most prevalent bacteria belonged to the genera Brochothrix (present in 80 % of biofilms), Pseudomonas and Psychrobacter (isolated from 70 % biofilms). From each biofilm we isolated bacteria from four to twelve different genera, indicating the presence of multi-species biofilms. This work ultimately determined the presence of multi-species biofilms within the meat processing environment, thereby identifying various sources of potential contamination. Especially the identification of biofilms in water hoses and associated parts highlights the need of a frequent monitoring at these sites. The knowledge gained about the presence and composition of biofilms (i.e. chemical and microbiological) will help to prevent and reduce biofilm formation within food processing environments.


Asunto(s)
Brochothrix/aislamiento & purificación , Manipulación de Alimentos , Carne/microbiología , Pseudomonas/aislamiento & purificación , Psychrobacter/aislamiento & purificación , Animales , Austria , Biopelículas/clasificación , Biopelículas/crecimiento & desarrollo , Bovinos , Desinfección/métodos , Microbiología de Alimentos , Enfermedades Transmitidas por los Alimentos/microbiología , Aves de Corral/microbiología , ARN Ribosómico 16S/análisis
2.
Poult Sci ; 99(3): 1297-1305, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-32111306

RESUMEN

The symbiosis of host and intestinal microbiota constitutes a microecosystem and plays an important role in maintaining intestinal homeostasis and regulating the host's immune system. Eimeria tenella, an obligate intracellular apicomplexan parasite, can cause coccidiosis, a serious intestinal disease. In this study, the effects of E. tenella infection on development parameters (villus height, crypt depth, mucosa thickness, muscularis thickness, and serosa thickness) and microbiota in chicken cecum were investigated. Fourteen-day-old male Hy-Line Variety Brown layer chickens were inoculated with sporulated oocysts of E. tenella. Cecal tissues were collected 7 d after inoculation. Relative density of goblet cells and glycoproteins were determined by Alcian blue periodic acid-Schiff staining and periodic acid-Schiff staining, respectively. Intestinal development parameters were also evaluated. Cecal contents were extracted, and the composition of cecal microflora was examined by Illumine sequencing in the V3-V4 region of the 16S rRNA gene. Results indicated that E. tenella infection destroyed the structure of cecal tissue and reduced the relative density of goblet cells and glycoproteins. Sequencing analysis indicated that E. tenella infection altered the diversity and composition of cecal microbiota. The populations of Proteobacteria, Enterococcus, Incertae, and Escherichia-Shigella decreased, and those of Bacteroidales and Rikenella significantly increased in the infected group compared with those in the control group. Hence, the pathological damage caused by E. tenella infection is associated with cecal microbiota dysbiosis, and this finding may be used to develop an alternative measure for alleviating the effect of coccidiosis on the poultry industry.


Asunto(s)
Pollos , Coccidiosis/veterinaria , Eimeria tenella/fisiología , Mucosa Intestinal/microbiología , Enfermedades de las Aves de Corral/parasitología , Animales , Ciego/microbiología , Coccidiosis/parasitología , Microbioma Gastrointestinal/efectos de los fármacos , Masculino , ARN Ribosómico 16S/análisis
3.
Zool Res ; 41(2): 188-193, 2020 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-32135580

RESUMEN

A new species of the genus Amolops, Amolops tuanjieensis sp. nov., is described from Yunnan, China. The new species can be distinguished by the following characters: dorsolateral folds present; dorsal and ventral surfaces smooth; top of head and dorsum brown-red with irregular gray and dark spots; flank green; side of head black, from tip of snout, diffusing posteriorly to axilla, continuing as black streak below edge of dorsolateral fold; SVL 39.5-40.4 mm in males, 56.8-60.7 mm in females; tympanum distinct; supratympanic fold indistinct; vomerine teeth in two oblique rows between choanae, closer to each other than choanae; vocal sacs present; nuptial pads present; outer metatarsal tubercle absent, supernumerary tubercles absent; all fingertips expanded into discs; limbs dorsally brown with dark brown bars and irregular dark brown blotches.


Asunto(s)
Ranidae/clasificación , Animales , China , Femenino , Masculino , Filogenia , ARN Ribosómico 16S/análisis , Ranidae/anatomía & histología
4.
Rev. Hosp. Ital. B. Aires (2004) ; 40(1): 17-24, mar. 2020. ilus
Artículo en Español | LILACS | ID: biblio-1100762

RESUMEN

Se estima que aproximadamente 100 trillones de microorganismos (incluidos bacterias, virus y hongos) residen en el intestino humano adulto y que el total del material genético del microbioma es 100 veces superior al del genoma humano. Esta comunidad, conocida como microbioma se adquiere al momento del nacimiento a través de la flora comensal de la piel, vagina y heces de la madre y se mantiene relativamente estable a partir de los dos años desempeñando un papel crítico tanto en el estado de salud como en la enfermedad. El desarrollo de nuevas tecnologías, como los secuenciadores de próxima generación (NGS), permiten actualmente realizar un estudio mucho más preciso de ella que en décadas pasadas cuando se limitaba a su cultivo. Si bien esto ha llevado a un crecimiento exponencial en las publicaciones, los datos sobre las poblaciones Latinoamérica son casi inexistentes. La investigación traslacional en microbioma (InTraMic) es una de las líneas que se desarrollan en el Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). Esta se inició en 2018 con la línea de cáncer colorrectal (CCR) en una colaboración con el Colorectal Cancer Research Group del Leeds Institute of Medical Research en el proyecto Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents. A fines de 2019 se cumplió el objetivo de comprobar la factibilidad de la recolección, envío y análisis de muestras de MBF en 5 continentes, incluyendo muestras provenientes de la Argentina, Chile, India y Vietnam. Luego de haber participado de capacitaciones en Inglaterra, se ha cumplido con el objetivo de la etapa piloto, logrando efectivizar la recolección, envío y análisis metagenómico a partir de la secuenciación de la región V4 del ARNr 16S. En 2019, la línea de enfermedad de hígado graso no alcohólico se sumó a la InTraMic iniciando una caracterización piloto en el marco de una colaboración con el laboratorio Novartis. Los resultados de ese estudio, así como el de cáncer colorrectal, están siendo enviados a publicación. En 2020, con la incorporación de la línea de trasplante alogénico de células progenitoras hematopoyéticas, fue presentado un proyecto para un subsidio del CONICET que ha superado la primera etapa de evaluación. En el presente artículo se brinda una actualización sobre la caracterización taxonómica de microbioma y se describen las líneas de investigación en curso. (AU)


It is estimated that approximately 100 trillion microorganisms (including bacteria, viruses, and fungi) reside in the adult human intestine, and that the total genetic material of the microbiome is 100 times greater than that of the human genome. This community, known as the microbiome, is acquired at birth through the commensal flora of the mother's skin, vagina, and feces and remains relatively stable after two years, playing a critical role in both the state of health and in disease. The development of new technologies, such as next-generation sequencers (NGS), currently allow for a much more precise study of it than in past decades when it was limited to cultivation. Although this has led to exponential growth in publications, data on Latin American populations is almost non-existent. Translational research in microbiome (InTraMic) is one of the lines developed at the Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). This started in 2018 with the Colorectal Cancer Line (CRC) in a collaboration with the Colorectal Cancer Research Group of the Leeds Institute of Medical Research in the project "Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents". At the end of 2019, the objective of verifying the feasibility of collecting, sending and analyzing MBF samples on 5 continents, including samples from Argentina, Chile, India and Vietnam, was met. After having participated in training in England, the objective of the pilot stage has been met, achieving the collection, delivery and metagenomic analysis from the sequencing of the V4 region of the 16S rRNA. In 2019, the non-alcoholic fatty liver disease line joined InTraMic, initiating a pilot characterization in the framework of a collaboration with the Novartis laboratory. The results of that study, as well as that of colorectal cancer, are being published. In 2020, with the incorporation of the allogeneic hematopoietic stem cell transplantation line, a project was presented for a grant from the CONICET that has passed the first stage of evaluation. This article provides an update on the taxonomic characterization of the microbiome and describes the lines of ongoing research. (AU)


Asunto(s)
Humanos , Investigación en Medicina Traslacional/organización & administración , Microbioma Gastrointestinal/genética , Trasplante Homólogo , Vietnam , Aztreonam/uso terapéutico , ARN Ribosómico 16S/análisis , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/microbiología , Neoplasias Colorrectales/epidemiología , Clasificación/métodos , Trasplante de Células Madre Hematopoyéticas , Metagenómica , Investigación en Medicina Traslacional/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/tendencias , Enfermedad del Hígado Graso no Alcohólico/genética , Enfermedad del Hígado Graso no Alcohólico/microbiología , Enfermedad del Hígado Graso no Alcohólico/patología , Enfermedad del Hígado Graso no Alcohólico/epidemiología , Microbioma Gastrointestinal/fisiología , India , América Latina , Sangre Oculta
5.
J Dairy Sci ; 103(4): 3459-3469, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32037172

RESUMEN

The purpose of this study was to determine the effect of intramammary pirlimycin on the fecal microbiome of dairy cattle. Primiparous heifers were enrolled and assigned to a treatment or control group at a ratio of 2:1. In part 1 of the study, treated heifers (T1) were given intramammary pirlimycin into one infected quarter once daily for 2 d at 24-h intervals, according to the label instructions. Control heifers received no treatment. In part 2 of the study, treated heifers (T2) were given intramammary pirlimycin into one infected quarter once daily for 8 d at 24-h intervals, according to the label instructions. All enrolled heifers (T1, T2, and control) had quarter-level milk samples aseptically collected for bacterial culture and fecal samples collected for 16S rRNA gene sequencing on d 0, 2, 7, 14, 21, and 28. Milk samples were plated on Columbia blood agar and incubated at 37°C for 24 h. Bacteria were identified using MALDI-TOF mass spectrometry. The DNA was extracted from feces using PowerFecal kits (Qiagen, Venlo, the Netherlands). The 16S rRNA gene amplicon library construction and sequencing was performed at the University of Missouri DNA Core facility. Testing for differences in fecal community composition was performed via one-way permutational multivariate ANOVA of Bray-Curtis and Jaccard similarities using Past 3.13 (https://folk.uio.no/ohammer/past/). Mean total count of operational taxonomic units and Chao1, Shannon, and Simpson α-diversity indices were determined and compared via t-test or Wilcoxon rank sum test. A treatment-dependent effect was present in the observed and predicted richness of feces from cows in the T1 group at d 2 posttreatment. Additionally, intramammary pirlimycin induced a significant change in the composition of the fecal microbiota by d 2 in the treated groups. Based on calculated intra-subject similarities, intramammary pirlimycin was associated with a significant acute change in the fecal microbiota of dairy heifers and that chance reversed when the antimicrobial exposure was brief, but sustained following longer exposure. Overall, intramammary pirlimycin administration affected the fecal microbiome of lactating dairy heifers. Further work is necessary to determine the effect of these changes on the heifer and the dairy environment as well as if treatment is influencing antimicrobial resistance among enteric and environmental bacteria.


Asunto(s)
Antibacterianos/farmacología , Bovinos/microbiología , Clindamicina/análogos & derivados , Heces/microbiología , Microbiota/efectos de los fármacos , Animales , Antibacterianos/administración & dosificación , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Clindamicina/administración & dosificación , Clindamicina/farmacología , Femenino , Lactancia , Glándulas Mamarias Animales , Mastitis Bovina/microbiología , Leche , Países Bajos , ARN Ribosómico 16S/análisis
6.
PLoS One ; 15(2): e0228560, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32027711

RESUMEN

Culture-independent characterization of microbial communities associated with popular plant model systems have increased our understanding of the plant microbiome. However, the integration of other model systems, such as duckweed, could facilitate our understanding of plant microbiota assembly and evolution. Duckweeds are floating aquatic plants with many characteristics, including small size and reduced plant architecture, that suggest their use as a facile model system for plant microbiome studies. Here, we investigated the structure and assembly of the duckweed bacterial microbiome. First, a culture-independent survey of the duckweed bacterial microbiome from different locations in New Jersey revealed similar phylogenetic profiles. These studies showed that Proteobacteria is a dominant phylum in the duckweed bacterial microbiome. To observe the assembly dynamics of the duckweed bacterial community, we inoculated quasi-gnotobiotic duckweed with wastewater effluent from a municipal wastewater treatment plant. Our results revealed that duckweed strongly shapes its bacterial microbiome and forms distinct associations with bacterial community members from the initial inoculum. Additionally, these inoculation studies showed the bacterial communities of different duckweed species were similar in taxa composition and abundance. Analysis across the different duckweed bacterial communities collected in this study identified a set of "core" bacterial taxa consistently present on duckweed irrespective of the locale and context. Furthermore, comparison of the duckweed bacterial community to that of rice and Arabidopsis revealed a conserved taxonomic structure between the duckweed microbiome and the terrestrial leaf microbiome. Our results suggest that duckweeds utilize similar bacterial community assembly principles as those found in terrestrial plants and indicate a highly conserved structuring effect of leaf tissue on the plant microbiome.


Asunto(s)
Araceae/microbiología , Microbiota , Filogenia , Hojas de la Planta/microbiología , Arabidopsis/microbiología , Bacterias/genética , New Jersey , Oryza/microbiología , Proteobacteria , ARN Ribosómico 16S/análisis , Aguas Residuales/microbiología
7.
Poult Sci ; 99(2): 1096-1106, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-32029146

RESUMEN

We studied the microbial profiles of the duodenum, jejunum, and ileum during different developmental stages in the duck using high-throughput sequencing of the bacterial 16S rRNA gene. We also investigated the differences in the microbiota in the duodenum, jejunum, and ileum at different developmental times. A correlation analysis was performed between the most abundant bacterial genera and the development of the small intestine. An analysis of alpha diversity indicated different species richness and bacterial diversity in the different small intestinal segments and at different development times. A beta diversity analysis indicated differences in the bacterial community compositions across time. In a weighted UniFrac principal coordinates analysis, the samples clustered into two categories, 2 to 4 wk and 6 to 10 wk, in the duodenum, jejunum, and ileum. Our results show that the small intestine is predominantly populated by the phyla Firmicutes, Bacteroidetes, and Proteobacteria throughout the developmental stages of the duck. The duodenum, jejunum, and ileum shared most of the bacterial phyla and genera present, although they showed significant differences in their relative abundances in the intestinal segments and developmental stages. They shared different bacterial taxa during development times and among different segments when the intergroup differences were analyzed. The genera Bacillus, Corynebacterium 1, Lactococcus, Sphingomonas, and Haliangium correlated moderately positively with the increase in bodyweight and the lengths and weights of the duodenum, jejunum, and ileum, and these genera may be considered important markers when assessing the heath of the intestinal microbiota in ducks. This study provides a foundation upon which to extend our knowledge of the diversity and composition of the duck microbiota and a basis for further studies of the management of the small intestinal microbiota and improvements in the health and production of ducks.


Asunto(s)
Bacterias/aislamiento & purificación , Patos/microbiología , Microbioma Gastrointestinal , Animales , Bacterias/clasificación , Patos/crecimiento & desarrollo , Duodeno/microbiología , Íleon/microbiología , Yeyuno/microbiología , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis
8.
Zebrafish ; 17(1): 38-47, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31994993

RESUMEN

Neotropical cichlids include hundreds of species whose taxonomy has benefited of molecular phylogeny and whose karyotype evolution has been related to the amount and distribution of different classes of repetitive sequences. This study provides the first integrative molecular (cytochrome c oxidase subunit 1 and 16S sequences) and cytogenetic analyses of wild samples of the green terror Andinoacara rivulatus, a cichlid naturally distributed in Ecuador and spread throughout the world as an aquarium pet. Molecular data revealed that sequences of green terror constitute a single monophyletic clade within the genus and allowed species attribution of uncertain samples previously cytogenetically analyzed. Chromosome number (2n = 48) conforms to the general trend observed within neotropical cichlids. However, mapping of different classes of repeated sequences (18S rDNA, 5S rDNA, U1 snDNA and telomeric) revealed the presence of features uncommon among representatives of these fishes, like multiple major rDNA sites, and suggested a recent occurrence of rearrangements (fusion/inversion) in two chromosome pairs.


Asunto(s)
Mapeo Cromosómico , Cíclidos/genética , ADN/análisis , Cariotipo , Filogenia , Secuencias Repetitivas de Ácidos Nucleicos , Animales , Ecuador , Complejo IV de Transporte de Electrones/análisis , Femenino , Masculino , ARN Ribosómico 16S/análisis , Análisis de Secuencia de ADN
9.
PLoS One ; 15(1): e0227053, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-31940381

RESUMEN

Vestimentiferan tubeworms are key taxa in deep-sea chemosynthetic habitats worldwide. As adults they obtain their nutrition through their sulfide-oxidizing bacterial endosymbionts, which are acquired from the environment. Although horizontal transmission should favor infections by various symbiotic microbes, the current paradigm holds that every tubeworm harbors only one endosymbiotic 16S rRNA phylotype. Although previous studies based on traditional Sanger sequencing have questioned these findings, population level high-throughput analyses of the symbiont 16S diversity are still missing. To get further insights into the symbiont genetic variation and uncover hitherto hidden diversity we applied state-of-the-art 16S-V4 amplicon sequencing to populations of the co-occurring tubeworm species Lamellibrachia barhami and Escarpia spicata that were collected during E/V Nautilus and R/V Western Flyer cruises to cold seeps in the eastern Pacific Ocean. In agreement with earlier work our sequence data indicated that L. barhami and E. spicata share one monomorphic symbiont phylotype. However, complementary CARD-FISH analyses targeting the 16S-V6 region implied the existence of an additional phylotype in L. barhami. Our results suggest that the V4 region might not be sufficiently variable to investigate diversity in the intra-host symbiont population at least in the analyzed sample set. This is an important finding given that this region has become the standard molecular marker for high-throughput microbiome analyses. Further metagenomic research will be necessary to solve these issues and to uncover symbiont diversity that is hidden below the 16S rRNA level.


Asunto(s)
Bacterias/clasificación , Poliquetos/clasificación , Poliquetos/microbiología , Animales , Bacterias/genética , Bacterias/metabolismo , Biodiversidad , Ecosistema , Complejo IV de Transporte de Electrones/genética , Sedimentos Geológicos , Océano Pacífico , Poliquetos/genética , Poliquetos/metabolismo , ARN Ribosómico 16S/análisis , Simbiosis
10.
Am J Obstet Gynecol ; 222(2): 154.e1-154.e10, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31421123

RESUMEN

BACKGROUND: Although the vaginal and urinary microbiomes have been increasingly well-characterized in health and disease, few have described the relationship between these neighboring environments. Elucidating this relationship has implications for understanding how manipulation of the vaginal microbiome may affect the urinary microbiome and treatment of common urinary conditions. OBJECTIVE: To describe the relationship between urinary and vaginal microbiomes using 16S rRNA gene sequencing. We hypothesized that the composition of the urinary and vaginal microbiomes would be significantly associated, with similarities in predominant taxa. STUDY DESIGN: This multicenter study collected vaginal swabs and catheterized urine samples from 186 women with mixed urinary incontinence enrolled in a parent study and 84 similarly aged controls. Investigators decided a priori that if vaginal and/or urinary microbiomes differed between continent and incontinent women, the groups would be analyzed separately; if similar, samples from continent and incontinent women would be pooled and analyzed together. A central laboratory sequenced variable regions 1-3 (v1-3) and characterized bacteria to the genus level. Operational taxonomic unit abundance was described for paired vaginal and urine samples. Pearson's correlation characterized the relationship between individual operational taxonomic units of paired samples. Canonical correlation analysis evaluated the association between clinical variables (including mixed urinary incontinence and control status) and vaginal and urinary operational taxonomic units, using the Canonical correlation analysis function in the Vegan package (R version 3.5). Linear discriminant analysis effect size was used to find taxa that discriminated between vaginal and urinary samples. RESULTS: Urinary and vaginal samples were collected from 212 women (mean age 53±11 years) and results from 197 paired samples were available for analysis. As operational taxonomic units in mixed urinary incontinence and control samples were related in canonical correlation analysis and since taxa did not discriminate between mixed urinary incontinence or controls in either vagina or urine, mixed urinary incontinence and control samples were pooled for further analysis. Canonical correlation analysis of vaginal and urinary samples indicated that that 60 of the 100 most abundant operational taxonomic units in the samples largely overlapped. Lactobacillus was the most abundant genus in both urine and vagina (contributing on average 53% to an individual's urine sample and 64% to an individual's vaginal sample) (Pearson correlation r=0.53). Although less abundant than Lactobacillus, other bacteria with high Pearson correlation coefficients also commonly found in vagina and urine included: Gardnerella (r=0.70), Prevotella (r=0.64), and Ureaplasma (r=0.50). Linear discriminant analysis effect size analysis identified Tepidimonas and Flavobacterium as bacteria that distinguished the urinary environment for both mixed urinary incontinence and controls as these bacteria were absent in the vagina (Tepidimonas effect size 2.38, P<.001, Flavobacterium effect size 2.15, P<.001). Although Lactobacillus was the most abundant bacteria in both urine and vagina, it was more abundant in the vagina (linear discriminant analysis effect size effect size 2.72, P<.001). CONCLUSION: Significant associations between vaginal and urinary microbiomes were demonstrated, with Lactobacillus being predominant in both urine and vagina. Abundance of other bacteria also correlated highly between the vagina and urine. This inter-relatedness has implications for studying manipulation of the urogenital microbiome in treating conditions such as urgency urinary incontinence and urinary tract infections.


Asunto(s)
Microbiota/genética , Sistema Urinario/microbiología , Orina/microbiología , Vagina/microbiología , Adulto , Burkholderiales , Estudios de Casos y Controles , Clostridiales , Análisis Discriminante , Escherichia , Femenino , Flavobacterium , Gardnerella , Humanos , Lactobacillus , Modelos Lineales , Persona de Mediana Edad , Prevotella , ARN Ribosómico 16S/análisis , Streptococcus , Ureaplasma , Incontinencia Urinaria
11.
Am J Physiol Endocrinol Metab ; 318(1): E52-E61, 2020 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-31770016

RESUMEN

Metformin is a widely prescribed antidiabetic agent, whereas Scutellaria baicalensis (SB) is a commonly used medicinal herb for treatment of type 2 diabetes (T2D). Gut microbiota is involved in pathophysiology of metabolic diseases including T2D, and intestinal microbiota may be one of the important therapeutic targets for the ailment. This study was conducted to investigate the effects of SB combined with metformin on treatment of T2D while evaluating changes in the gut microbiota composition. Patients with T2D were randomized into control and treatment groups. Subjects who had already been prescribed metformin were allotted to additional SB (3.52 g/day) group or placebo group. The initial treatment session was 8 wk, and after washout period for 4 wk they were crossed over to the opposite treatment for another 8 wk. The influence of SB and placebo on the intestinal microbiota was analyzed by MiSeq system based on 16S rRNA gene. Glucose tolerance was lower in the SB group than the placebo group. Similarly, the relative RNA expression of TNF-α was significantly reduced after SB treatment. SB treatment influenced the gut microbiota, especially Lactobacillus and Akkermansia, which showed remarkable increases after SB treatment. Some subjects showed high liver enzyme levels after SB treatment, and their microbiota composition at baseline differed with subjects whose liver enzymes were not affected. We also predicted that selenocompound metabolism was increased and naphthalene degradation was decreased after SB treatment. These results suggest that SB with metformin treatment may improve the glucose tolerance and inflammation and influence the gut microbiota community in T2D.


Asunto(s)
Glucemia/metabolismo , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Microbioma Gastrointestinal , Hipoglucemiantes/uso terapéutico , Metformina/uso terapéutico , Extractos Vegetales/uso terapéutico , Adulto , Anciano , Alanina Transaminasa/metabolismo , Aspartato Aminotransferasas , Estudios Cruzados , Diabetes Mellitus Tipo 2/metabolismo , Diabetes Mellitus Tipo 2/microbiología , Método Doble Ciego , Quimioterapia Combinada , Femenino , Microbioma Gastrointestinal/genética , Prueba de Tolerancia a la Glucosa , Hemoglobina A Glucada/metabolismo , Humanos , Insulina/metabolismo , Resistencia a la Insulina , Interleucina-6/genética , Lactobacillus , Masculino , Persona de Mediana Edad , ARN Mensajero/metabolismo , ARN Ribosómico 16S/análisis , Scutellaria baicalensis , Factor de Necrosis Tumoral alfa/genética , Verrucomicrobia , Adulto Joven
12.
Food Chem ; 305: 125431, 2020 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-31610425

RESUMEN

Recent European regulations require safety assessments of food enzymes (FE) before their commercialization. FE are mainly produced by micro-organisms, whose viable strains nor associated DNA can be present in the final products. Currently, no strategy targeting such impurities exists in enforcement laboratories. Therefore, a generic strategy of first line screening was developed to detect and identify, through PCR amplification and sequencing of the 16S-rRNA gene, the potential presence of FE producing bacteria in FE preparations. First, the specificity was verified using all microbial species reported to produce FE. Second, an in-house database, with 16S reference sequences from bacteria producing FE, was constructed for their fast identification through blast analysis. Third, the sensitivity was assessed on a spiked FE preparation. Finally, the applicability was verified using commercial FE preparations. Using straightforward PCR amplifications, Sanger sequencing and blast analysis, the proposed strategy was demonstrated to be convenient for implementation in enforcement laboratories.


Asunto(s)
Bacterias/aislamiento & purificación , Código de Barras del ADN Taxonómico , ARN Ribosómico 16S/análisis , Bacterias/genética , Bacterias/metabolismo , Manipulación de Alimentos , Reacción en Cadena de la Polimerasa
13.
Food Chem ; 309: 125653, 2020 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-31670116

RESUMEN

This study used DNA barcoding and DNA mini-barcoding to test a variety of animal-derived food products sold in the Chinese market for potential mislabeling. Samples (52) including meat, poultry, and fish purchased from retail and online sources were examined. Regions of cytochrome C oxidase I (COI) gene (~650 bp) and 16S rRNA (~220 bp) were used as full- and mini-barcode markers, respectively. Approximately 94% (49 of 52) of the samples generated barcode sequences. The failure rate for full COI full-barcodes was 44%, but we obtained the 16S rRNA mini-barcode from 87% of the COI-failed cases. Overall, the survey revealed that 23% (12 of 52) of animal-derived products were mislabeled and, in most cases, contain undeclared species. Thus, regulatory measures and continuous monitoring for mislabeling of animal-derived products should be conducted.


Asunto(s)
Código de Barras del ADN Taxonómico/métodos , ADN/análisis , Peces/genética , Aves de Corral/genética , Animales , China , ADN/aislamiento & purificación , ADN/metabolismo , Complejo IV de Transporte de Electrones/análisis , Complejo IV de Transporte de Electrones/genética , Complejo IV de Transporte de Electrones/metabolismo , Carne/análisis , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/metabolismo
14.
Am J Physiol Gastrointest Liver Physiol ; 318(2): G361-G369, 2020 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-31869241

RESUMEN

Longer colonic transit time and hard stools are associated with increased gut microbiota diversity. Here, we investigate to what extent quantitative measures of (segmental) colonic transit time were related to gut microbiota composition, microbial metabolites, and gut-related parameters in a human cross-sectional study. Using radiopaque markers, (segmental) colonic transit time (CTT) was measured in 48 lean/overweight participants with long colonic transit but without constipation. Fecal microbiota composition was determined using 16S rRNA gene amplicon sequencing. Associations between gastrointestinal transit (segmental CTT and stool frequency and consistency), microbiota diversity and composition, microbial metabolites [short-chain fatty acids (SCFA), branched-chain fatty acids, and breath hydrogen], habitual diet, and gut-related host parameters [lipopolysaccharide-binding protein (LBP) and fecal calprotectin] were investigated using univariate and multivariate approaches. Long descending (i.e., distal) colonic transit was associated with increased microbial α-diversity but not with stool consistency. Using unweighted and weighted UniFrac distance, microbiota variation was not related to (segmental) CTT but to demographics, diet, plasma LBP, and fecal calprotectin. Bray-Curtis dissimilarity related only to stool consistency. Rectosigmoid and descending colonic transit were negatively associated with fecal SCFA and plasma acetate, respectively. This study suggests that the distal colon transit may affect not only microbiota diversity but also microbial metabolism.NEW & NOTEWORTHY We extend previous findings showing that long distal colonic transit time influences microbial diversification and fermentation, whereas stool consistency is related to microbiota composition in humans with a long colonic transit. This study puts the importance of the (distal) colonic site in microbiota ecology forward, which should be considered in future therapeutic studies targeting, for instance, short-chain fatty acid production to improve metabolic health.


Asunto(s)
Colon/fisiopatología , Microbioma Gastrointestinal , Tránsito Gastrointestinal , Adulto , Envejecimiento/fisiología , Colon/microbiología , Estudios Transversales , Dieta , Ácidos Grasos Volátiles/análisis , Heces/microbiología , Femenino , Fermentación , Motilidad Gastrointestinal , Humanos , Complejo de Antígeno L1 de Leucocito/análisis , Lipopolisacáridos/metabolismo , Masculino , Persona de Mediana Edad , Sobrepeso/fisiopatología , ARN Ribosómico 16S/análisis , Caracteres Sexuales , Adulto Joven
15.
Chemosphere ; 245: 125615, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31864063

RESUMEN

Understanding environmental factors driving ecological processes of archaeal communities in heavily contaminated rivers is crucial for improvements in river ecological monitoring and indication. However, succession mechanisms underlying vertical and horizontal archaeal community assemblages in contaminated rivers remains largely unstudied. Here, to investigate ecological processes controlling archaeal community succession in a contaminated urban river, multivariate statistics approaches were applied to fields samples collected from locations representing vertical and horizontal assemblages of archaeal community. Our results revealed that archaeal community in the river showed distinct vertical and horizontal distribution patterns and the differences between water and sediment samples were most significant. Beta-diversity patterns in the vertical and horizontal assemblages are both almost completely caused by species replacement between sampling points (horizontal ßSIM = 0.60 ± 0.09, ßNES = 0.09 ± 0.05; vertical ßSIM = 0.40 ± 0.07, ßNES = 0.10 ± 0.06). Considering phylogenetic turnover deviation, homogenizing dispersal was the most crucial process dominating archaeal community assemblages in water samples while main ecological process in sediment samples was variable selection. Euryarchaeota and Thaumarchaeota were found to prefer high-nutrients and low-nutrients environments, respectively. Analysis of environmental drivers of archaeal phyla distribution and community assemblages indicated that nutrients played a decisive role in driving the sediment archaeal community. Dissolved oxygen (DO) explained the most variation in phylogenetic turnover deviation within all water archaeal community while oxidation reduction potential (ORP) contributed most for horizontal sediment archaeal community assemblages. These findings help to indicate the pollution situation of the river and provide information to predict how archaeal communities would respond to different environmental variations.


Asunto(s)
Archaea/fisiología , Ecología , Sedimentos Geológicos/microbiología , Microbiota , Filogenia , Ríos/química , Archaea/genética , Oxidación-Reducción , Oxígeno , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética , Contaminación del Agua
16.
PLoS One ; 14(12): e0226186, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31834903

RESUMEN

Gastrointestinal microbiota has significant impact on the nutrition and health of monogastric herbivores animals including donkey. However, so far the microbiota in different gastrointestinal compartments of healthy donkey has not been described. Therefore, we investigated the abundance and function of microbiota at different sites of the gastrointestinal tract (GIT) (foregut: stomach, duodenum, jejunum and ileum; hindgut: cecum, ventral colon, dorsal colon, and rectum) of healthy adult donkeys mainly based on 16S rRNA gene sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. Collectively, our results showed that donkey has a rich, diverse and multi-functional microbiota along the GIT. In general, the richness and diversity of the microbiota are much higher in the hindgut relative to that in the foregut; at phylum level, the Firmicutes is dominant in the foregut while both Firmicutes and Bacteroides are abundant in the hindgut; at the genus level, Lactobacillus was dominant in the foregut while Streptococcus was more dominant in the hindgut. Our further PICRUSt analysis showed that varying microbiota along the GIT is functionally compatible with the corresponding physiological function of different GIT sites. For example, the microbes in the foregut are more active at carbohydrate metabolism, and in the hindgut are more active at amino acid metabolism. This work at the first time characterized the donkey digestive system from the aspects of microbial composition and function, provided an important basic data about donkey healthy gastrointestinal microbiota, which may be utilized to evaluate donkey health and also offer clues to further investigate donkey digestive system, nutrition, even to develop the microbial supplements.


Asunto(s)
Bacterias/clasificación , ADN Bacteriano/análisis , Microbioma Gastrointestinal/genética , Tracto Gastrointestinal/microbiología , Animales , Bacterias/genética , ADN Bacteriano/genética , Equidae , Masculino , Filogenia , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética
17.
BMC Pulm Med ; 19(1): 260, 2019 Dec 23.
Artículo en Inglés | MEDLINE | ID: mdl-31870355

RESUMEN

BACKGROUND: The emergence of multi-drug resistant pathogens is an urgent health-related problem, and the appropriate use of antibiotics is imperative. It is often difficult to identify the causative bacteria in patients with aspiration pneumonia because tracheal aspirate contains contaminants of oral bacteria. We investigated the dynamics of microbiota in mechanically ventilated patients with aspiration pneumonia to develop a treatment strategy. METHODS: Twenty-two intubated patients with aspiration pneumonia were recruited. Saliva and tracheal aspirate of the subjects were collected at three time points: (A) within 2 h after intubation, (B) just before administration of antibiotics, and (C) 48-72 h after administration of antibiotics. The microbiota in each specimen was analyzed by using the 16S rRNA gene clone library sequencing method. Bacterial floras of the samples were analyzed by principal component analysis. RESULTS: Principal component analysis based on the composition of genus revealed that although the changes of microbiota in the saliva from (A) to (B) were not clear, the composition of anaerobes in the tracheal aspirate (B) was lower than (A). In fact, the reduction of anaerobes, not in the saliva but in the tracheal aspirate from (A) to (B), was confirmed by incident rate ratios estimated by a multilevel Poisson regression model (p < 0.001). The extent of decrease in anaerobes was fully dependent on the time difference between the sampling of tracheal aspirate (A) and (B)-in particular, over 3 h of mechanical ventilation. This indicates that the alterations of microbiota (involving the reduction of anaerobes in the lower respiratory tract) occurred during mechanical ventilation prior to the administration of antibiotics. After the administration of antibiotics, Enterobacter spp., Corynebacterium spp., Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, and Granulicatera adiacens were predominantly detected in the tracheal aspirate (C). CONCLUSION: The microbiota of the lower respiratory tract changes dynamically during mechanical ventilation and during the administration of antibiotics in intubated patients with aspiration pneumonia. Antibiotics should be selected on the premise that dynamic changes in microbiota (involved in the reduction of anaerobes) may occur during the mechanical ventilation in these patients.


Asunto(s)
Antibacterianos/uso terapéutico , Microbiota/genética , Neumonía por Aspiración/tratamiento farmacológico , Respiración Artificial , Saliva/microbiología , Tráquea/microbiología , Carnobacteriaceae , Corynebacterium , Enterobacter , Femenino , Humanos , Klebsiella pneumoniae , Masculino , Boca/microbiología , Neumonía por Aspiración/microbiología , Análisis de Componente Principal , Pseudomonas aeruginosa , ARN Ribosómico 16S/análisis , Staphylococcus aureus
18.
PLoS One ; 14(12): e0226239, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31841551

RESUMEN

Bacteria and other types of microbes interact with their hosts in several ways, including metabolic pathways, development, and complex behavioral processes such as mate recognition. During the mating season, adult males of the lesser long-nosed agave pollinator bat Leptonycteris yerbabuenae (Phyllostomidae: Glossophaginae) develop a structure called the dorsal patch, which is located in the interscapular region and may play a role in kin recognition and mate selection. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, we identified a total of 2,847 microbial phylotypes in the dorsal patches of eleven specimens. Twenty-six phylotypes were shared among all the patches, accounting for 30 to 75% of their relative abundance. These shared bacteria are distributed among 13 families, 10 orders, 6 classes and 3 phyla. Two of these common bacterial components of the dorsal patch are Lactococcus and Streptococcus. Some of them-Helcococcus, Aggregatibacter, Enterococcus, and Corynebacteriaceae-include bacteria with pathogenic potential. Half of the shared phylotypes belong to Gallicola, Anaerococcus, Peptoniphilus, Proteus, Staphylococcus, Clostridium, and Peptostreptococcus and specialize in fatty acid production through fermentative processes. This work lays the basis for future symbiotic microbe studies focused on communication and reproduction strategies in wildlife.


Asunto(s)
Quirópteros/fisiología , Microbiota/fisiología , Conducta Sexual Animal/fisiología , Animales , Dorso/microbiología , Bacterias/genética , Bacterias/aislamiento & purificación , Biodiversidad , Quirópteros/microbiología , ADN Bacteriano/análisis , Secuenciación de Nucleótidos de Alto Rendimiento , Masculino , México , Microbiota/genética , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética , Reproducción/fisiología
19.
BMC Vet Res ; 15(1): 468, 2019 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-31864369

RESUMEN

BACKGROUND: Horses that undergo surgery for treatment of primary large colon disease have been reported to be at increased risk of developing recurrent colic episodes postoperatively. The reasons for this are currently unknown. The aim of the current study was to characterise the faecal microbiota of horses with colic signs associated with primary large colon lesions treated surgically and to compare the composition of their faecal microbiota to that of a control group of horses undergoing emergency orthopaedic treatment. Faecal samples were collected from horses in both groups on admission to hospital, during hospitalisation and following discharge from hospital for a total duration of 12 weeks. Additionally, colonic content samples were collected from surgical colic patients if pelvic flexure enterotomy was performed during laparotomy. A total of 12 samples were collected per horse. DNA was extracted from samples using a commercial kit. Amplicon mixtures were created by PCR amplification of the V1 - V2 regions of the bacterial 16S rRNA genes and submitted for sequencing using the Ion Torrent PGM next-generation sequencing system. Multivariate data analysis was used to characterise the faecal microbiota and to investigate differences between groups. RESULTS: Reduced species richness was evident in the colonic samples of the colic group compared to concurrent sampling of the faeces. Alpha and beta diversity differed significantly between the faecal and colonic microbiota with 304 significantly differentially abundant OTUs identified. Only 46 OTUs varied significantly between the colic and control group. There were no significant differences in alpha and beta diversity of faecal microbiota between colic and control horses at admission. However, this lack of significant differences between groups should be interpreted with caution due to a small sample size. CONCLUSIONS: The results of the current study suggest that faecal samples collected at hospital admission in colic cases may not accurately represent changes in upper gut microbiota in horses with colic due to large colon disease.


Asunto(s)
Cólico/veterinaria , Enfermedades del Colon/veterinaria , Heces/microbiología , Microbioma Gastrointestinal , Enfermedades de los Caballos/cirugía , Animales , Cólico/microbiología , Cólico/cirugía , Enfermedades del Colon/microbiología , Enfermedades del Colon/cirugía , Enfermedades de los Caballos/microbiología , Caballos , ARN Ribosómico 16S/análisis
20.
J Aquat Anim Health ; 31(4): 320-327, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31743945

RESUMEN

The aim of the present study was to characterize two gram-negative bacterial strains that were isolated from diseased Atlantic Horse Mackerel Trachurus trachurus in 2017. Based on the results obtained from the biochemical and chemotaxonomic characterization, the isolates were identified as Lacinutrix spp. The highest similarity of the 16S rRNA gene sequences was obtained with the strain L. venerupis CECT 8573T (99.1%), while other species showed similarities of 98% (L. jangbogonensis) and 97% (L. algicola and L. mariniflava). Molecular characterization by repetitive element (REP)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR, as well as proteomic characterization by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), demonstrated heterogeneity between the strains from the Atlantic Horse Mackerel and the type strain, CECT 8573T . The virulence of one of the isolates for Turbot Scophthalmus maximus, European Sea Bass Dicentrarchus labrax, Senegalese Sole Solea senegalensis, and Rainbow Trout Oncorhynchus mykiss was assessed under experimental conditions. No mortalities were recorded after intraperitoneal injections with high doses of bacteria (1 × 109  CFU/mL). Thus, further studies are necessary to elucidate the impact of this bacterial species as a fish pathogen.


Asunto(s)
Enfermedades de los Peces/microbiología , Infecciones por Flavobacteriaceae/veterinaria , Flavobacteriaceae/aislamiento & purificación , Flavobacteriaceae/patogenicidad , Perciformes/microbiología , Animales , Peces/microbiología , Flavobacteriaceae/fisiología , Infecciones por Flavobacteriaceae/microbiología , Inyecciones Intraperitoneales/veterinaria , ARN Bacteriano/análisis , ARN Ribosómico 16S/análisis , Virulencia
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