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1.
Intern Med ; 59(17): 2089-2094, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32879200

RESUMO

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


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Hipertensão Portal/microbiologia , Cirrose Hepática/complicações , Adulto , Bactérias/genética , Bifidobacterium/isolamento & purificação , Clostridium/isolamento & purificação , Varizes Esofágicas e Gástricas/etiologia , Feminino , Humanos , Hipertensão Portal/etiologia , Intestinos/microbiologia , Masculino , Pessoa de Meia-Idade , Probióticos/uso terapêutico , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Streptococcus/isolamento & purificação
2.
Medicine (Baltimore) ; 99(37): e21788, 2020 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-32925716

RESUMO

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


Assuntos
Carcinoma Hepatocelular/microbiologia , Microbioma Gastrointestinal , Fatores Imunológicos/uso terapêutico , Imunoterapia/mortalidade , Neoplasias Hepáticas/microbiologia , Idoso , Bacteroides/crescimento & desenvolvimento , Carcinoma Hepatocelular/tratamento farmacológico , Carcinoma Hepatocelular/mortalidade , China , Faecalibacterium/crescimento & desenvolvimento , Feminino , Humanos , Imunoterapia/métodos , Neoplasias Hepáticas/tratamento farmacológico , Neoplasias Hepáticas/mortalidade , Masculino , Pessoa de Meia-Idade , Intervalo Livre de Progressão , Estudos Prospectivos , RNA Ribossômico 16S/análise , Resultado do Tratamento
3.
Mol Genet Genomics ; 295(6): 1517-1528, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32803300

RESUMO

Increasing studies have revealed strong links among gut microbiota, health status, and shrimp development, but they mainly focus on the microbiota of Pacific white shrimp, Penaeus vannamei, during life stages from juveniles to adults. Little is known about shrimp microbiota dynamics at early developmental stages. In this study, with an aim to profile shrimp microbiota and its dynamics at stages nauplius, zoea, mysis, and early postlarva, we conducted a survey for the successful breeding processes in a commercial hatchery in China, sampled 33 samples including larval/postlarval shrimp, suspended substance in rearing water (SSRW), and nutrition supplements (i.e., algae and brine shrimp larvae) at stages N5, Z2, M2, and P2. The associated bacterial communities were sequenced and comparatively analyzed using high-throughput sequencing of bacterial 16S rRNA genes. Our case study results showed that bacterial community structures and compositions were strikingly different at stages N5, Z2, and P2, indicating the shift of microbiota at the three stages. Many taxa within Gamma-, Alphaproteobacteria, and Flavobacteriia classes were observed to be stage-specifically abundant and identified as taxonomic biomarkers potentially used to differentiate among shrimp at different early developmental stages. Summing up, these results shed light on larval/postlarval microbiota and its dynamics at different early developmental stages, highlighting the potential roles of shrimp development in microbiota formation and shifting.


Assuntos
Bactérias/classificação , Bactérias/genética , Larva/microbiologia , Microbiota/genética , Penaeidae/microbiologia , RNA Ribossômico 16S/análise , Animais , Bactérias/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Larva/crescimento & desenvolvimento , Metagenômica , Penaeidae/crescimento & desenvolvimento , Tanques , RNA Ribossômico 16S/genética
4.
Int J Food Microbiol ; 328: 108668, 2020 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-32474228

RESUMO

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.


Assuntos
Brochothrix/isolamento & purificação , Manipulação de Alimentos , Carne/microbiologia , Pseudomonas/isolamento & purificação , Psychrobacter/isolamento & purificação , Animais , Áustria , Biofilmes/classificação , Biofilmes/crescimento & desenvolvimento , Bovinos , Desinfecção/métodos , Microbiologia de Alimentos , Doenças Transmitidas por Alimentos/microbiologia , Aves Domésticas/microbiologia , RNA Ribossômico 16S/análise
5.
PLoS One ; 15(6): e0235235, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32598345

RESUMO

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.


Assuntos
Monitoramento Ambiental/métodos , Água Subterrânea/análise , Água Subterrânea/microbiologia , Microbiota , Água do Mar/análise , Água do Mar/microbiologia , Golfo do México , Hidrologia , RNA Ribossômico 16S/análise , Movimentos da Água
6.
Biomed Environ Sci ; 33(5): 306-314, 2020 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-32553074

RESUMO

Objective: High PM 2.5 concentration is the main feature of increasing haze in developing states, but information on its microbial composition remains very limited. This study aimed to determine the composition of microbiota in PM 2.5 in Guangzhou, a city located in the tropics in China. Methods: In Guangzhou, from March 5 th to 10 th, 2016, PM 2.5 was collected in middle volume air samplers for 23 h daily. The 16S rDNA V4 region of the PM 2.5 sample extracted DNA was investigated using high-throughput sequence. Results: Among the Guangzhou samples, Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Actinobacteria were the dominant microbiota accounting for more than 90% of the total microbiota, and Stenotrophomonas was the dominant gram-negative bacteria, accounting for 21.30%-23.57%. We examined the difference in bacterial distribution of PM 2.5 between Beijing and Guangzhou at the genus level; Stenotrophomonas was found in both studies, but Escherichia was only detected in Guangzhou. Conclusion: In conclusion, the diversity and specificity of microbial components in Guangzhou PM 2.5 were studied, which may provide a basis for future pathogenicity research in the tropics.


Assuntos
Microbiologia do Ar , Poluentes Atmosféricos/análise , Bactérias/isolamento & purificação , Microbiota , Material Particulado/análise , Bactérias/classificação , China , Cidades , Monitoramento Ambiental , Tamanho da Partícula , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
7.
Biomed Environ Sci ; 33(4): 248-259, 2020 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-32438962

RESUMO

Objective: Our objective was to investigate the occurrence of opportunistic pathogens and characterize the bacterial community structures in the water system of a pulmonary hospital. Methods: The water samples were collected from automatic and manual faucets in the consulting room, treatment room, dressing room, respiratory ward, and other non-medical rooms in three buildings of the hospital. Quantitative polymerase chain reaction was used to quantify the load of several waterborne opportunistic pathogens and related microorganisms, including Legionella spp., Mycobacterium spp., and M. avium. Illumina sequencing targeting 16S rRNA genes was performed to profile bacterial communities. Results: The occurrence rates of Legionella spp., Mycobacterium spp., and M. avium were 100%, 100%, and 76%, respectively in all samples. Higher occurrence rates of M. avium were observed in the outpatient service building (building 1, 91.7%) and respiration department and wards (building 2, 80%) than in the office building (building 3), where no M. avium was found. M. avium were more abundant in automatic faucets (average 2.21 × 10 4 gene copies/L) than in manual faucets (average 1.03 × 10 4 gene copies/mL) ( P < 0.01). Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Acidobacteria were the dominant bacterial phyla. Disinfectant residuals, nitrate, and temperature were found to be the key environmental factors driving microbial community structure shifts in water systems. Conclusion: This study revealed a high level of colonization of water faucets by opportunistic pathogens and provided insight into the characteristics of microbial communities in a hospital water system and approaches to reduce risks of microbial contamination.


Assuntos
Água Potável/microbiologia , Legionella/isolamento & purificação , Microbiota , Mycobacterium/isolamento & purificação , Qualidade da Água , China , Genes Bacterianos , Hospitais , Mycobacterium avium/isolamento & purificação , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Abastecimento de Água
8.
J Vet Diagn Invest ; 32(3): 369-381, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32306863

RESUMO

Microcystis is a widespread freshwater cyanobacterium that can produce microcystin, a potent hepatotoxin harmful to animals and humans. Therefore, it is crucial to monitor for the presence of toxigenic Microcystis spp. to provide early warning of potential microcystin contamination. Microscopy, which has been used traditionally to identify Microcystis spp., cannot differentiate toxigenic from non-toxigenic Microcystis. We developed a PCR-based method to detect toxigenic Microcystis spp. based on detection of the microcystin synthetase C (mcyC) gene and 16S rRNA gene. Specificity was validated against toxic and nontoxic M. aeruginosa strains, as well as 4 intergeneric freshwater cyanobacterial strains. Analytical sensitivity was as low as 747 fg/µL genomic DNA (or 3 cells/µL) for toxic M. aeruginosa. Furthermore, we tested 60 water samples from 4 farm ponds providing drinking water to swine facilities in the midwestern United States using this method. Although all water samples were positive for Microcystis spp. (i.e., 16S rRNA gene), toxigenic Microcystis spp. were detected in only 34 samples (57%). Seventeen water samples contained microcystin (0.1-9.1 µg/L) determined with liquid chromatography-mass spectrometry, of which 14 samples (82%) were positive for mcyC. A significant correlation was found between the presence of toxigenic Microcystis spp. and microcystin in water samples (p = 0.0004). Our PCR method can be a low-cost molecular tool for rapid and specific identification of toxigenic Microcystis spp. in farm ponds, improving detection of microcystin contamination, and ensuring water safety for farm animals.


Assuntos
Microcistinas/isolamento & purificação , Microcystis/isolamento & purificação , Reação em Cadeia da Polimerase/veterinária , Tanques/microbiologia , Proteínas de Bactérias/análise , Toxinas Bacterianas/análise , Eutrofização , Fazendas , Meio-Oeste dos Estados Unidos , Reação em Cadeia da Polimerase/métodos , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
9.
Rev. Hosp. Ital. B. Aires (2004) ; 40(1): 17-24, mar. 2020. ilus
Artigo em Espanhol | LILACS | ID: biblio-1100762

RESUMO

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)


Assuntos
Humanos , Pesquisa Médica Translacional/organização & administração , Microbioma Gastrointestinal/genética , Transplante Homólogo , Vietnã , Aztreonam/uso terapêutico , RNA Ribossômico 16S/análise , Neoplasias Colorretais/genética , Neoplasias Colorretais/microbiologia , Neoplasias Colorretais/epidemiologia , Classificação/métodos , Transplante de Células-Tronco Hematopoéticas , Metagenômica , Pesquisa Médica Translacional/métodos , Sequenciamento de Nucleotídeos em Larga Escala/tendências , Hepatopatia Gordurosa não Alcoólica/genética , Hepatopatia Gordurosa não Alcoólica/microbiologia , Hepatopatia Gordurosa não Alcoólica/patologia , Hepatopatia Gordurosa não Alcoólica/epidemiologia , Microbioma Gastrointestinal/fisiologia , Índia , América Latina , Sangue Oculto
10.
Poult Sci ; 99(3): 1297-1305, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32111306

RESUMO

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.


Assuntos
Galinhas , Coccidiose/veterinária , Eimeria tenella/fisiologia , Mucosa Intestinal/microbiologia , Doenças das Aves Domésticas/parasitologia , Animais , Ceco/microbiologia , Coccidiose/parasitologia , Microbioma Gastrointestinal/efeitos dos fármacos , Masculino , RNA Ribossômico 16S/análise
11.
Zool Res ; 41(2): 188-193, 2020 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-32135580

RESUMO

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.


Assuntos
Ranidae/classificação , Animais , China , Feminino , Masculino , Filogenia , RNA Ribossômico 16S/análise , Ranidae/anatomia & histologia
12.
Appl Environ Microbiol ; 86(9)2020 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-32111585

RESUMO

Pathogenic bacteria in wastewater are generally considered to be efficiently removed in biological wastewater treatment plants. This understanding is almost solely based on culture-based control measures, and here we show, by applying culture-independent methods, that the removal of species in the genus Arcobacter was less effective than for many other abundant genera in the influent wastewater. Arcobacter was one of the most abundant genera in influent wastewater at 14 municipal wastewater treatment plants and was also abundant in the "clean" effluent from all the plants, reaching up to 30% of all bacteria as analyzed by 16S rRNA gene amplicon sequencing. Metagenomic analyses, culturing, genome sequencing of Arcobacter isolates, and visualization by fluorescent in situ hybridization (FISH) confirmed the presence of the human-pathogenic Arcobacter cryaerophilus and A. butzleri in both influent and effluent. The main reason for the high relative abundance in the effluent was probably that Arcobacter cells, compared to those of other abundant genera in the influent, did not flocculate and attach well to the activated sludge flocs, leaving a relatively large fraction dispersed in the water phase. The study shows there is an urgent need for new standardized culture-independent measurements of pathogens in effluent wastewaters, e.g., amplicon sequencing, and an investigation of the problem on a global scale to quantify the risk for humans and livestock.IMPORTANCE The genus Arcobacter was unexpectedly abundant in the effluent from 14 Danish wastewater treatment plants treating municipal wastewater, and the species included the human-pathogenic A. cryaerophilus and A. butzleri Recent studies have shown that Arcobacter is common in wastewater worldwide, so the study indicates that discharge of members of the genus Arcobacter may be a global problem, and further studies are needed to quantify the risk and potentially minimize the discharge. The study also shows that culture-based analyses are insufficient for proper effluent quality control, and new standardized culture-independent measurements of effluent quality encompassing most pathogens should be considered.


Assuntos
Arcobacter/isolamento & purificação , Eliminação de Resíduos Líquidos , Águas Residuárias/microbiologia , Dinamarca , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
13.
J Fish Dis ; 43(5): 551-559, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32196691

RESUMO

In June 2019, massive mortalities of cultured Penaeus vannamei occurred in a local farm in Hainan Province, China. The diseased shrimp displayed evident black gills. Three bacterial strains 20190611001, 20190611007 and 20190611022 were isolated from hepatopancreas and gills of the diseased shrimp and identified as Photobacterium damselae subsp. damselae based on the sequence analysis of 16S rRNA and toxR genes. These three isolates showed haemolytic activities. Of them, strain 20190611022 isolated from hepatopancreas was selected and processed for pathogenic analysis. The calculated median lethal dose (LD50 ) was 9.75 ± 4.29 × 105 CFU/g (body weight) by challenging P. vannameivia reverse gavage. The diseased shrimp displayed enlarged hepatopancreatic tubules and sloughing of epithelial cells in tubular lumens. The strain 20190611022 was also characterized by the testing of API 20NE systems and antibiotic susceptibility. The results of disc diffusion test showed that strain 20190611022 was sensitive to chloramphenicol, compound sulfamethoxazole, cefoperazone, ceftriaxone, ceftazidime and cefuroxime. To our knowledge, this is the first report of isolation and characterization of Photobacterium damselae subsp. damselae from natural diseased P. vannamei. Our findings can serve as a basis for further studies of its pathogenicity and provide technological support for disease controlling in shrimp aquaculture.


Assuntos
Penaeidae/microbiologia , Photobacterium/fisiologia , Animais , Proteínas de Bactérias/análise , China , Proteínas de Ligação a DNA/análise , Brânquias/microbiologia , Photobacterium/isolamento & purificação , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Fatores de Transcrição/análise
14.
Aliment Pharmacol Ther ; 51(8): 770-780, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32133670

RESUMO

BACKGROUND: Incidence and mortality of gastric cancer (GC) are high in Mongolia despite Helicobacter pylori in the Mongolian population being less virulent. AIM: To evaluate gastric bacterial microbiota profiles in patients with GC and its precursor histological conditions. METHODS: We conducted a case-control study among 48 GC and 120 noncancer patients (20 normal gastric mucosa [control], 20 gastritis, 40 with atrophy and 40 intestinal metaplasia [IM]). We performed 16S rRNA gene amplicon sequencing and compared taxonomic and functional prediction profiles based on the diagnosis group and H pylori infection status. RESULTS: The highest overall bacterial alpha diversity metrics were observed in the control group, followed by the IM and cancer groups. The gastritis and atrophy groups had the least diversity. Lactobacilli and Enterococci were the dominant genus in several cancer patients especially in the absence of H pylori. In addition, Carnobacterium, Glutamicibacter, Paeniglutamicibacter, Fusobacterium and Parvimonas were associated with GC regardless of H pylori infection. Firmicutes were decreased in the gastritis and atrophy groups and increased in the IM and cancer groups. The functional metabolic activity of the Embden-Meyerhof-Parnas pathway and the utilization of sugar, were significantly increased in cancer group compared with the noncancer group. CONCLUSION: Microbial factors other than H pylori may play a role in Mongolian GC. We identified novel associations between GC and the genera Enterococcus, Lactobacillus, Carnobacterium, Glutamicibacter, Paeniglutamicibacter, Fusobacterium, and Parvimonas.


Assuntos
Mucosa Gástrica/patologia , Microbioma Gastrointestinal , Lesões Pré-Cancerosas/epidemiologia , Lesões Pré-Cancerosas/microbiologia , Neoplasias Gástricas/epidemiologia , Neoplasias Gástricas/microbiologia , Adulto , Idoso , Grupo com Ancestrais do Continente Asiático/estatística & dados numéricos , Estudos de Casos e Controles , Estudos Transversais , Feminino , Mucosa Gástrica/microbiologia , Gastrite/epidemiologia , Gastrite/microbiologia , Microbioma Gastrointestinal/genética , Infecções por Helicobacter/complicações , Infecções por Helicobacter/epidemiologia , Helicobacter pylori/genética , Humanos , Incidência , Masculino , Metaplasia/complicações , Metaplasia/epidemiologia , Metaplasia/patologia , Pessoa de Meia-Idade , Mongólia/epidemiologia , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética , Neoplasias Gástricas/patologia
15.
Poult Sci ; 99(3): 1515-1527, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32111319

RESUMO

Enterotypes are used to describe clusters of specific gut microbial community structures, but few reports exist on the identification of enterotypes in poultry. In addition, there is incomplete understanding on the role of the foregut microbiota in the digestion and absorption of nutrients in poultry. Thus, this study aimed to identify the duodenal enterotypes by examining microbial communities from 206 broilers using 16S rRNA high-throughput sequencing and explore the effects of enterotypes on phenotypic performance and nutrient metabolism with metabolomics. The duodenal microbial communities of the broiler population were partitioned into 3 enterotypes (ET1, ET2, and ET3), and significant differences were observed in α-diversity among the enterotypes (P < 0.01). At the genus level, the ET1 group was over-represented by Bacteroides (9.8%) and Escherichia-Shigella (8.9%), the ET2 group was over-represented by Ochrobactrum (19.4%) and Rhodococcus (14.7%), and the ET3 group was over-represented by Bacillus (23.4%) and Akkermansia (16.2%). The relative abundance of the dominant taxa of each enterotype was significantly higher than that in the other 2 enterotypes (P < 0.01). The results showed that Ochrobactrum and Rhodococcus were positively correlated with cellobiose, alpha-D-glucose, D-mannose, and D-allose (r = 0.429, 0.435, 0.482, and 0.562, respectively; all P < 0.05). Rhodococcus was also positively correlated with tridecanoic acid and glycerol 1-myristate (r = 0.655 and 0.489, respectively; all P < 0.01). In terms of phenotype, the triglyceride level in the ET2 group was significantly higher than that in the ET1 group (P < 0.05), and the subcutaneous fat thickness and abdominal fat weight in the ET2 group were the highest (P > 0.05). Taken together, these results confirmed the presence of enterotypes in broilers and found that the dominant microbes in broilers of the ET2 group might play a major role in the degradation and utilization of plant polysaccharides, which may have an impact on the serum triglyceride level and fat deposition in broilers. These findings lay a foundation for further studies on the gut microbial interactions with the metabolism in broilers and the regulation of the gut microbiota to promote growth and well-being in broilers.


Assuntos
Bactérias/isolamento & purificação , Galinhas/microbiologia , Duodeno/microbiologia , Microbiota , Nutrientes/metabolismo , Fenótipo , Animais , Bactérias/classificação , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Masculino , Metabolômica , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
16.
Poult Sci ; 99(2): 1096-1106, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32029146

RESUMO

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.


Assuntos
Bactérias/isolamento & purificação , Patos/microbiologia , Microbioma Gastrointestinal , Animais , Bactérias/classificação , Patos/crescimento & desenvolvimento , Duodeno/microbiologia , Íleo/microbiologia , Jejuno/microbiologia , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
17.
PLoS One ; 15(2): e0228560, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32027711

RESUMO

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.


Assuntos
Araceae/microbiologia , Microbiota , Filogenia , Folhas de Planta/microbiologia , Arabidopsis/microbiologia , Bactérias/genética , New Jersey , Oryza/microbiologia , Proteobactérias , RNA Ribossômico 16S/análise , Águas Residuárias/microbiologia
18.
Am J Obstet Gynecol ; 223(2): 248.e1-248.e21, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32017922

RESUMO

BACKGROUND: There is controversy about whether the amniotic fluid contains bacteria. With the use of sequencing-based methods, recent studies report that the amniotic fluid is colonized by microorganisms. However, background-contaminating DNA might lead to false-positive findings when such a low microbial biomass sample is examined. OBJECTIVE: The purpose of this study was to determine whether the midtrimester amniotic fluid of patients who subsequently had normal pregnancy outcomes contains a microbial signature. STUDY DESIGN: In this prospective cohort study, 42 amniotic fluid samples were collected from 37 pregnancies (5 twin and 32 singletons) during genetic amniocentesis in the midtrimester. The subsequent pregnancy outcomes of all the participants were followed. Multiple methods were used to detect the presence of microorganisms in this study, which included cultivation, quantitative real-time polymerase chain reaction, and 16S ribosomal RNA gene sequencing. Multiple positive control samples (n=16) served as quality control samples and included 3 adult fecal samples, 4 vaginal swabs, and 9 artificial bacterial communities that were run in parallel with negative control samples (n=12) that included 4 samples from the hospital operating room and 8 samples from the laboratory, to account for background-contaminating DNA during each step of the experiments. RESULTS: No bacteria under anaerobic or aerobic conditions or genital mycoplasmas were cultured from any of the amniotic fluid samples. Quantitative polymerase chain reaction did not reveal greater copy numbers of 16S ribosomal RNA gene in amniotic fluid samples than in negative control samples. 16S Ribosomal RNA gene sequencing did not indicate a significant difference in the microbial richness or community structures between amniotic fluid and negative control samples. CONCLUSION: With multiple methods of microbiologic inquiry, no microorganisms were identified in the midtrimester amniotic fluid of healthy pregnancies with a normal pregnancy outcome.


Assuntos
Líquido Amniótico/microbiologia , Técnicas de Cultura/métodos , Segundo Trimestre da Gravidez , RNA Ribossômico 16S/análise , Reação em Cadeia da Polimerase em Tempo Real/métodos , Adulto , Amniocentese , Líquido Amniótico/imunologia , Corioamnionite/epidemiologia , Estudos de Coortes , Citocinas/análise , Citocinas/imunologia , Feminino , Ruptura Prematura de Membranas Fetais/epidemiologia , Humanos , Gravidez , Resultado da Gravidez , Nascimento Prematuro/epidemiologia , Estudos Prospectivos
19.
Poult Sci ; 99(2): 1174-1184, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32036968

RESUMO

Owing to the practical interest in understanding duration of fertility (DF) to reduce the cost of producing hatching eggs by decreasing the frequency of artificial insemination, as well to uncover the mechanism of the estrogen-gut microbiome axis, elucidating the interaction between the maternal microbiome and the function of sperm storage tubules (SST) has become important for revealing the DF in laying hens. In this study, we investigated the compositional, structural, and functional differences in gut microbiomes between hens with high (HSST, n = 8) and low SST activity (LSST, n = 10) by performing phenotypic selection from approximately 400 individual hens based on their DFs. Their cecal microbial communities were analyzed by sequencing the V4 region of the 16S rRNA gene. The microbiome abundance estimators from the ceca of HSST and LSST hens were not significantly different at the phylum and genus taxonomic levels, although the relative abundances for the phylum Firmicutes and the genus Lactobacillus were higher in the HSST group. Furthermore, some taxonomic levels of bacteria expressing the components of several metabolic pathways differed between the HSST and LSST groups. Moreover, predicting functional microbiomes by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that certain pathways, such as the metabolism of carbohydrates and protein, cellular processes, and organismal systems, of the HSST group exhibited higher expression of genes associated with bioactivity and energy biosynthesis than those in the LSST group. Our results may provide insights into hen-microbe interactions with respect to DF and will be useful in establishing a strategy for new research to uncover the functional regulation of SST in laying hens.


Assuntos
Galinhas/fisiologia , Fertilidade , Microbioma Gastrointestinal , Inseminação Artificial/veterinária , Espermatozoides/fisiologia , Criação de Animais Domésticos , Animais , Ceco/microbiologia , Galinhas/genética , Feminino , Masculino , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
20.
J Dairy Sci ; 103(4): 3459-3469, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32037172

RESUMO

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.


Assuntos
Antibacterianos/farmacologia , Bovinos/microbiologia , Clindamicina/análogos & derivados , Fezes/microbiologia , Microbiota/efeitos dos fármacos , Animais , Antibacterianos/administração & dosagem , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Clindamicina/administração & dosagem , Clindamicina/farmacologia , Feminino , Lactação , Glândulas Mamárias Animais , Mastite Bovina/microbiologia , Leite , Países Baixos , RNA Ribossômico 16S/análise
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