PCR Conditions for 16S Primers for Analysis of Microbes in the Colon of Rats

Guillén, Isabel; Camacho, Hanlet; Tuero, Ángela; Bacardí, Dania; Palenzuela, Daniel; Aguilera, A.; Silva, J A; Estrada, Regla; Gell, Omar; Suárez, José; Ancízar, Julio; Brown, Enma; Colarte, Amanda B; Castro, José María Albertos; Novoa, Lidia I

doi:10.7171/jbt.16-2703-002

Cited by 5 publications

(3 citation statements)

References 14 publications

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“…The specific primer pairs were as follows: for Escherichia spp., 5′-GTTAATACCTTTGCTCATTGA-3′ and 5′-ACCAGGGTATCTAATCCTGTT-3′ (35); for Bacillus spp., 5′-CAGTAGGGAATCTTCCGCAATG-3′ and 5′-AGCCGTGGCTTTCTGGT-3′ (36). A universal primer pair for all bacteria was also used: 5′-GTGGTGCACGGCTGTCGTCA-3′ and 5′-ACGTCATCCACACCTTCCTC-3′ (37).…”

Section: Methodsmentioning

confidence: 99%

Suppression of Obesity by an Intestinal Helminth through Interactions with Intestinal Microbiota

et al. 2019

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Obesity is increasingly causing lifestyle diseases in developed countries where helminthic infections are rarely seen. Here, we investigated whether an intestinal nematode, Heligmosomoides polygyrus, has a suppressive role in diet-induced obesity in mice. Infection with H. polygyrus suppressed weight gain in obese mice, which was associated with increased uncoupling protein 1 (UCP1) expression in adipocytes and a higher serum norepinephrine (NE) concentration. Blocking interactions of NE with its receptor on adipocytes resulted in the failure to prevent weight gain and to enhance UCP1 expression in obese mice infected with H. polygyrus, indicating that NE is responsible for the protective effects of H. polygyrus on obesity. In addition to sympathetic nerve-derived NE, the intestinal microbiota was involved in the increase in NE. Infection with H. polygyrus altered the composition of intestinal bacteria, and antibiotic treatment to reduce intestinal bacteria reversed the higher NE concentration, UCP1 expression, and prevention of the weight gain observed after H. polygyrus infection. Our data indicate that H. polygyrus exerts suppressive roles on obesity through modulation of microbiota that produce NE.

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Section: Methodsmentioning

confidence: 99%

Suppression of Obesity by an Intestinal Helminth through Interactions with Intestinal Microbiota

et al. 2019

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“…After sequencing, the identified bases and the predicted quality of each base were converted into raw data for analysis. In this step, BCL/cBCL files were converted into FASTQ (http://www.bioinformatics.babraham.ac.uk/projects/fastqc (accessed on 15 May 2022)) files using the Illumina package bcl2fastq [20].…”

Section: Whole Genome Sequencing and Analysis Workflowmentioning

confidence: 99%

Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia

Alghamdi,

Al-Judaibi,

Al-Rashede

et al. 2023

Microorganisms

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Multidrug-resistant (MDR) bacteria are one of the most serious threats to public health, and one of the most important types of MDR bacteria are those that are acquired in a hospital, known as nosocomial. This study aimed to isolate and identify MDR bacteria from selected hospitals in Jeddah and analyze their antibiotic-resistant genes. Bacteria were collected from different sources and wards of hospitals in Jeddah City. Phoenix BD was used to identify the strains and perform susceptibility testing. Identification of selected isolates showing MDR to more than three classes on antibiotics was based on 16S rRNA gene and whole genome sequencing. Genes conferring resistance were characterized using de novo and pan-genome analyses. In total, we isolated 108 bacterial strains, of which 75 (69.44%) were found to be MDR. Taxonomic identification revealed that 24 (32%) isolates were identified as Escherichia coli, 19 (25.3%) corresponded to Klebsiella pneumoniae, and 17 (22.67%) were methicillin-resistant Staphylococcus aureus (MRSA). Among the Gram-negative bacteria, K. pneumoniae isolates showed the highest resistance levels to most antibiotics. Of the Gram-positive bacteria, S. aureus (MRSA) strains were noticed to exhibit the uppermost degree of resistance to the tested antibiotics, which is higher than that observed for K. pneumoniae isolates. Taken together, our results illustrated that MDR Gram-negative bacteria are the most common cause of nosocomial infections, while MDR Gram-positive bacteria are characterized by a wider antibiotic resistance spectrum. Whole genome sequencing found the appearance of antibiotic resistance genes, including SHV, OXA, CTX-M, TEM-1, NDM-1, VIM-1, ere(A), ermA, ermB, ermC, msrA, qacA, qacB, and qacC.

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“…The primers for the amplification of the 16S gene were designed based on the conserved regions in the 518F-800R and 27F-1492R genome sequences (Guillen et al 2016). Library size was determined to verify the size of the PCR-enriched fragments, and the template size was checked for distribution by running on an Agilent Technologies 2100 bioanalyzer using a DNA 1000 chip.…”

Section: Molecular Identification Of Microbial Community Of Hot Springsmentioning

confidence: 99%

Microbial diversity and abundance in the hot springs on the west coast of Saudi Arabia as a potential source of novel industrial products

AlSaade

Ashy

Al-Fassi

et al. 2022

MBJ

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A knowledge gap exists regarding the potential of thermophilic bacteria in the hot springs in Saudi Arabia as a resource for medically useful compounds. This study aimed to investigate the microbial diversity in the soils of hot springs at three locations on the west coast of Saudi Arabia, including Jizan, Al Lith, and Tabuk. Soil samples were extracted for rDNA 16S, and the results were analysed for microbial diversity and abundance. The results showed the dominance of Acidobacteriota, Actinobacteriota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Nitrospirota, and Thermotogota. Actinobacteriota dominated the microbial population in Al Lith soil, while Deinococcota were dominant in Jizan soil and Chloroflexi in Tabuk soil. Firmicutes and Proteobacteria had high microbial populations in all three soils. Based on principal coordinate analysis, the normalized relative microbial diversity of all soils showed differences as well as similarities in the distribution of taxonomic classifications between soil samples. In conclusion, the microbial diversity in Jizan, Al Lith, and Tabuk included a variety of microorganism species that can potentially be used in biotechnology as a novel source for industrial production of medically useful compounds.

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PCR Conditions for 16S Primers for Analysis of Microbes in the Colon of Rats

Cited by 5 publications

References 14 publications

Suppression of Obesity by an Intestinal Helminth through Interactions with Intestinal Microbiota

Suppression of Obesity by an Intestinal Helminth through Interactions with Intestinal Microbiota

Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia

Microbial diversity and abundance in the hot springs on the west coast of Saudi Arabia as a potential source of novel industrial products

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