Molecular Identification of Polyhydroxyalkanoates-Producing Bacteria Isolated from Enriched Microbial Community

Polyhydroxyalkanoates (PHAs) are especially interesting because of their similar properties to synthetic plastics and their potential use as biodegradable polymers. Many strategies have been employed to effectively and economically produce PHAs, among them a production process based on mixed microbial populations, enriched from activated sludge could be one of the alternative technologies. Defining the bacterial species creating these anonymous populations is crucial for the improvement of cultivation strategy. Moreover, enriched bacterial populations could be a promising source for microbes, useful in many biotechnological projects. The main object of this study was to characterize the microorganisms creating the microbial consortium cultured towards PHAs production. After cultivation, bacteria were identified using the 16S rRNA gene sequencing approach. The presence of genes engaged in PHAs synthesis was detected using PCR. The performed analysis revealed that among eleven isolated bacterial strains, four possessed the ability of polyhydroxybutyrate synthesis.

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Isolation and characterisation of endocrine disruptor nonylphenol-using bacteria from South Africa

South African Journal of Science ◽

10.17159/sajs.2017/20160287 ◽

2017 ◽

Vol 113 (5/6) ◽

Author(s):

Lehlohonolo B. Qhanya ◽

Ntsane T. Mthakathi ◽

Charlotte E. Boucher ◽

Samson S. Mashele ◽

Chrispian W. Theron ◽

...

Keyword(s):

South Africa ◽

Bacterial Species ◽

Endocrine Disrupting Chemicals ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Strains ◽

Mpumalanga Province ◽

Synthetic Chemicals ◽

Phylogenetic Identification ◽

Rrna Gene Sequencing

Endocrine disrupting chemicals (EDCs) are synthetic chemicals that alter the function of endocrine systems in animals including humans. EDCs are considered priority pollutants and worldwide research is ongoing to develop bioremediation strategies to remove EDCs from the environment. An understanding of indigenous microorganisms is important to design efficient bioremediation strategies. However, much of the information available on EDCs has been generated from developed regions. Recent studies have revealed the presence of different EDCs in South African natural resources, but, to date, studies analysing the capabilities of microorganisms to utilise/degrade EDCs have not been reported from South Africa. Here, we report for the first time on the isolation and enrichment of six bacterial strains from six different soil samples collected from the Mpumalanga Province, which are capable of utilising EDC nonylphenol as a carbon source. Furthermore, we performed a preliminary characterisation of isolates concerning their phylogenetic identification and capabilities to degrade nonylphenol. Phylogenetic analysis using 16S rRNA gene sequencing revealed that four isolates belonged to Pseudomonas and the remaining two belonged to Enterobacteria and Stenotrophomonas. All six bacterial species showed degradation of nonylphenol in broth cultures, as HPLC analysis revealed 41–46% degradation of nonylphenol 12 h after addition. The results of this study represent the beginning of identification of microorganisms capable of degrading nonylphenol, and pave the way for further exploration of EDC-degrading microorganisms from South Africa.

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Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

Animals ◽

10.3390/ani11010031 ◽

2020 ◽

Vol 11 (1) ◽

pp. 31

Author(s):

Elisa Cotozzolo ◽

Paola Cremonesi ◽

Giulio Curone ◽

Laura Menchetti ◽

Federica Riva ◽

...

Keyword(s):

Digestive Tract ◽

Large Intestine ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Productive Performance ◽

Bacterial Populations ◽

Bacterial Microbiota ◽

Rrna Gene Sequencing

The microbiota is extremely important for the animal’s health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.

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Bacterial Populations in International Artisanal Kefirs

Microorganisms ◽

10.3390/microorganisms8091318 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1318 ◽

Cited By ~ 2

Author(s):

Abrar Sindi ◽

Md. Bahadur Badsha ◽

Gülhan Ünlü

Keyword(s):

Bacterial Species ◽

Dairy Product ◽

16S Rrna Gene Sequencing ◽

Acetic Acid Bacteria ◽

Lactobacillus Helveticus ◽

Rrna Gene ◽

Bacterial Populations ◽

Health Promoting ◽

Rrna Gene Sequencing ◽

Fermented Dairy

Artisanal kefir is a traditional fermented dairy product made using kefir grains. Kefir has documented natural antimicrobial activity and health benefits. A typical kefir microbial community includes lactic acid bacteria (LAB), acetic acid bacteria, and yeast among other species in a symbiotic matrix. In the presented work, the 16S rRNA gene sequencing was used to reveal bacterial populations and elucidate the diversity and abundance of LAB species in international artisanal kefirs from Fusion Tea, Britain, the Caucuses region, Ireland, Lithuania, and South Korea. Bacterial species found in high abundance in most artisanal kefirs included Lactobacillus kefiranofaciens, Lentilactobacillus kefiri,Lactobacillus ultunensis, Lactobacillus apis, Lactobacillus gigeriorum, Gluconobacter morbifer, Acetobacter orleanensis, Acetobacter pasteurianus, Acidocella aluminiidurans, and Lactobacillus helveticus. Some of these bacterial species are LAB that have been reported for their bacteriocin production capabilities and/or health promoting properties.

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Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco

Agronomy ◽

10.3390/agronomy11071344 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1344

Author(s):

Naima Lemjiber ◽

Khalid Naamani ◽

Annabelle Merieau ◽

Abdelhi Dihazi ◽

Nawal Zhar ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Genomic Islands ◽

Rrna Gene ◽

In Planta ◽

Bacterial Strains ◽

Bacillus Altitudinis ◽

Genes Encoding ◽

Bacillus Spp ◽

Pear Trees ◽

Rrna Gene Sequencing

Bacterial burn is one of the major diseases affecting pear trees worldwide, with serious impacts on producers and economy. In Morocco, several pear trees (Pyrus communis) have shown leaf burns since 2015. To characterize the causal agent of this disease, we isolated fourteen bacterial strains from different parts of symptomatic pear trees (leaves, shoots, fruits and flowers) that were tested in planta for their pathogenicity on Louise bonne and Williams cultivars. The results showed necrotic lesions with a significant severity range from 47.63 to 57.77% on leaves of the Louise bonne cultivar inoculated with isolate B10, while the other bacterial isolates did not induce any disease symptom. 16S rRNA gene sequencing did not allow robust taxonomic discrimination of the incriminated isolate. Thus, we conducted whole-genome sequencing (WGS) and phylogenetic analyzes based on gyrA, gyrB and cdaA gene sequences, indicating that this isolate belongs to the Bacillus altitudinis species. This taxonomic classification was further confirmed by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) analyzes compared to sixty-five Bacillus spp. type strains. The genome was mined for genes encoding carbohydrate-active enzymes (CAZymes) known to play a role in the vegetal tissue degradation. 177 candidates with functions that may support the in planta phytopathogenicity results were identified. To the best of our knowledge, this is the first data reporting B. altitudinis as agent of leaf burn in P. communis in Morocco. Our dataset will improve our knowledge on spread and pathogenicity of B. altitudinis genotypes that appears as emergent phytopathogenic agent, unveiling virulence factors and their genomic location (i.e., within genomic islands or the accessory genome) to induce trees disease.

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Evaluation of Commercial Disinfectants against Staphylococcus lentus and Micrococcus spp. of Poultry Origin

Veterinary Medicine International ◽

10.1155/2020/8811540 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Otun Saha ◽

Nadira Naznin Rakhi ◽

Arif Istiaq ◽

Israt Islam ◽

Munawar Sultana ◽

...

Keyword(s):

Micrococcus Luteus ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Average Diameter ◽

Diffusion Method ◽

Dilution Method ◽

Rrna Gene ◽

Poultry Farms ◽

Rrna Gene Sequencing ◽

Selection Of

Introduction. Effective sanitation strategies for poultry farms require an appropriate selection of the disinfectant based on the contaminants present and their sensitivity to the disinfectants. Aim. The current study investigated the prevalence of streptococci/micrococci in poultry farms of Bangladesh and the efficacy of commercial disinfectants (Savlon, Lysol, Quatovet, Virkon S, and Virocid) along with alcohol against these pathogens to adopt appropriate strategies. Materials and Methods. Conventional approaches and the 16S rRNA gene sequencing were performed to confirm the isolates at the species level along with microtiter biofilm assay to determine their biofilm-forming ability. Efficacy of the disinfectants was tested against those isolates using agar well diffusion and minimum inhibitory concentration (MIC) test by broth dilution method using different dilutions of the disinfectants. Results. Staphylococcus lentus (n = 32), Micrococcus luteus (n = 7), and Micrococcus aloeverae (n = 4) were confirmed among 102 presumptively screened streptococci/micrococci isolates from 43 samples. No single disinfectant showed equally high efficacy against all three bacterial species in agar well diffusion test, although Virocid showed the lowest MIC against all three of them. Lysol was least effective among the commercial disinfectants by both MIC and diffusion method, although each commercial disinfectant was more effective than alcohol. Considering both the average diameter of the inhibition zones and the MIC values, efficacy can be interpreted as Virocid > Quatovet > Savlon > Virkon S > Lysol. Although the efficacy decreased with decreasing concentration, the disinfectants retained a satisfactory level of efficacy at 50% concentration. Among test pathogens, M. aloeverae was the most sensitive to the disinfectants and the weakest biofilm producers, whereas 4/14 S. lentus and 1/5 M. luteus were strong biofilm producers, which may cause more reduction in the efficacy in environmental conditions. Conclusion. As no ideal disinfectant was found in the study, the efficacy of the disinfectants should be routinely evaluated and validated to ensure the sanitation standards in the poultry sector.

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Xylanolytic Psychotrophs From Andosolic Sedge Fens and Moss Heaths in Iceland

Fine Focus ◽

10.33043/ff.4.2.171-186 ◽

2018 ◽

Vol 4 (2) ◽

pp. 171-186

Author(s):

Olivia J. Rickman ◽

M. Auður Sigurbjörnsdóttir ◽

Oddur Vilhemsson

Keyword(s):

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Strains ◽

Cold Environments ◽

Specific Pcr ◽

Xylanolytic Activity ◽

Cold Active ◽

Rrna Gene Sequencing ◽

Stenotrophomonas Rhizophila

Nine xylanolytic bacterial strains were isolated from fen and heath soils in northern Iceland. They were found by 16S rRNA gene sequencing to belong to the genera Paenibacillus, Bacillus, Pseudomonas, and Stenotrophomonas. Using a simple, plate-based semiquantitative assay with azo-crosslinked xylan as the substrate, it was determined that although isolated from cold environments, most of the strains displayed greater xylanolytic activity under mesophilic conditions, with only the paenibacilli displaying markedly cold-active xylanolytic activity. Indeed, for one isolate, Paenibacillus castaneae OV2122, xylanolytic activity was only detected at 15°C and below under the conditions tested. Of the nine strains, Paenibacillus amylolyticus OV2121 displayed the greatest activity at 5°C. Glycohydrolase family-specific PCR indicated that the paenibacilli produced multiple xylanases of families 10 and 11, whereas a family 8 xylanase was detected in Pseudomonas kilonensis AL1515, and a family 11 xylanase in Stenotrophomonas rhizophila AL1610.

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Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters

Frontiers in Microbiology ◽

10.3389/fmicb.2021.634025 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sarah Zecchin ◽

Simona Crognale ◽

Patrizia Zaccheo ◽

Stefano Fazi ◽

Stefano Amalfitano ◽

...

Keyword(s):

Microbial Communities ◽

Inorganic Arsenic ◽

16S Rrna Gene Sequencing ◽

Northern Italy ◽

Rrna Gene ◽

Bacterial Populations ◽

Main Driver ◽

Rrna Gene Sequencing ◽

Arsenite Oxidizing Bacteria ◽

Card Fish

Arsenic mobilization in groundwater systems is driven by a variety of functionally diverse microorganisms and complex interconnections between different physicochemical factors. In order to unravel this great ecosystem complexity, groundwaters with varying background concentrations and speciation of arsenic were considered in the Po Plain (Northern Italy), one of the most populated areas in Europe affected by metalloid contamination. High-throughput Illumina 16S rRNA gene sequencing, CARD-FISH and enrichment of arsenic-transforming consortia showed that among the analyzed groundwaters, diverse microbial communities were present, both in terms of diversity and functionality. Oxidized inorganic arsenic [arsenite, As(III)] was the main driver that shaped each community. Several uncharacterized members of the genus Pseudomonas, putatively involved in metalloid transformation, were revealed in situ in the most contaminated samples. With a cultivation approach, arsenic metabolisms potentially active at the site were evidenced. In chemolithoautotrophic conditions, As(III) oxidation rate linearly correlated to As(III) concentration measured at the parental sites, suggesting that local As(III) concentration was a relevant factor that selected for As(III)-oxidizing bacterial populations. In view of the exploitation of these As(III)-oxidizing consortia in biotechnology-based arsenic bioremediation actions, these results suggest that contaminated aquifers in Northern Italy host unexplored microbial populations that provide essential ecosystem services.

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Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

Journal of Burn Care & Research ◽

10.1093/jbcr/irab244 ◽

2022 ◽

Author(s):

Chen Zheng-li ◽

Peng Yu ◽

Wu Guo-sheng ◽

Hong Xu-Dong ◽

Fan Hao ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Community Structure ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Sprague Dawley ◽

Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

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Early-Life Intake of an Isotonic Protein Drink Improves the Gut Microbial Profile of Piglets

Animals ◽

10.3390/ani10050879 ◽

2020 ◽

Vol 10 (5) ◽

pp. 879

Author(s):

Stefan G. Buzoianu ◽

Ava M. Firth ◽

CallaBria Putrino ◽

Fabio Vannucci

Keyword(s):

Environmental Changes ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Bacterial Populations ◽

E Coli ◽

Microbial Profile ◽

Before And After ◽

Potential Alternative ◽

Rrna Gene Sequencing

A healthy microbial community in the gut of piglets is critical to minimize the negative performance consequences associated with dietary and environmental changes that occur at weaning. Tonisity Px, an isotonic protein drink, is a potential alternative to balance the gut microbiota as it contains key ingredients for nourishing the small intestine. In the present study, 16 litters comprising 161 piglets were randomly allocated to a group to which Tonisity Px was provided from days 2 to 8 of age (TPX group) or to a control group, to which no Tonisity Px was provided. The TPX group also received Tonisity Px in the 3 days before and after weaning. At days 9, 17, and 30 of age, fecal and ileum samples were collected from piglets belonging to both groups and analyzed using 16S rRNA gene sequencing, semiquantitative PCR of Rotavirus serogroups, and semiquantitative Escherichia coli culture. Overall, Tonisity Px increased the abundance of beneficial bacterial populations (Lactobacillus and Bacteroides species) and reduced potentially pathogenic bacterial populations (E. coli and Prevotellaceae), in both the pre-weaning and post-weaning periods.

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Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽

10.1128/msphere.00187-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

Shinya Kageyama ◽

Mikari Asakawa ◽

Toru Takeshita ◽

Yukari Ihara ◽

Shunsuke Kanno ◽

...

Keyword(s):

Oral Cavity ◽

Bacterial Diversity ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Bacterial Composition ◽

Content Type ◽

Operational Taxonomic Units ◽

Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

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