Bacterial Communities in the Embryo of Maize Landraces: Relation with Susceptibility to Fusarium Ear Rot

Locally adapted maize accessions (landraces) represent an untapped resource of nutritional and resistance traits for breeding, including the shaping of distinct microbiota. Our study focused on five different maize landraces and a reference commercial hybrid, showing different susceptibility to fusarium ear rot, and whether this trait could be related to particular compositions of the bacterial microbiota in the embryo, using different approaches. Our cultivation-independent approach utilized the metabarcoding of a portion of the 16S rRNA gene to study bacterial populations in these samples. Multivariate statistical analyses indicated that the microbiota of the embryos of the accessions grouped in two different clusters: one comprising three landraces and the hybrid, one including the remaining two landraces, which showed a lower susceptibility to fusarium ear rot in field. The main discriminant between these clusters was the frequency of Firmicutes, higher in the second cluster, and this abundance was confirmed by quantification through digital PCR. The cultivation-dependent approach allowed the isolation of 70 bacterial strains, mostly Firmicutes. In vivo assays allowed the identification of five candidate biocontrol strains against fusarium ear rot. Our data revealed novel insights into the role of the maize embryo microbiota and set the stage for further studies aimed at integrating this knowledge into plant breeding programs.

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Beneficial Microorganisms to Control the Gray Mold of Grapevine: From Screening to Mechanisms

Microorganisms ◽

10.3390/microorganisms9071386 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1386

Author(s):

Zakaria Amarouchi ◽

Qassim Esmaeel ◽

Lisa Sanchez ◽

Cédric Jacquard ◽

Majida Hafidi ◽

...

Keyword(s):

In Silico Analysis ◽

Antimicrobial Effect ◽

Gray Mold ◽

Vitis Vinifera L ◽

Rrna Gene ◽

Bacterial Strains ◽

In Vivo Test ◽

Chemical Products ◽

Silico Analysis

In many vineyards around the world, Botrytis cinerea (B. cinerea) causes one of the most serious diseases of aerial grapevine (Vitis vinifera L.) organs. The control of the disease relies mainly on the use of chemical products whose use is increasingly challenged. To develop new sustainable methods to better resist B. cinerea, beneficial bacteria were isolated from vineyard soil. Once screened based on their antimicrobial effect through an in vivo test, two bacterial strains, S3 and S6, were able to restrict the development of the pathogen and significantly reduced the Botrytis-related necrosis. The photosynthesis analysis showed that the antagonistic strains also prevent grapevines from considerable irreversible PSII photo-inhibition four days after infection with B. cinerea. The 16S rRNA gene sequences of S3 exhibited 100% similarity to Bacillus velezensis, whereas S6 had 98.5% similarity to Enterobacter cloacae. On the other hand, the in silico analysis of the whole genome of isolated strains has revealed the presence of “biocontrol-related” genes supporting their plant growth and biocontrol activities. The study concludes that those bacteria could be potentially useful as a suitable biocontrol agent in harvested grapevine.

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

Polish Journal of Microbiology ◽

10.33073/pjm-2013-005 ◽

2013 ◽

Vol 62 (1) ◽

pp. 45-50 ◽

Cited By ~ 4

Author(s):

SŁAWOMIR CIESIELSKI ◽

TOMASZ POKOJ ◽

JUSTYNA MOŻEJKO ◽

EWA KLIMIUK

Keyword(s):

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Strains ◽

Bacterial Populations ◽

Alternative Technologies ◽

Cultivation Strategy ◽

Rrna Gene Sequencing ◽

Promising Source ◽

Potential Use

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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In-vivo Efficacy of Poultry and Fish Probiotics on Green Mussel, Perna viridis, Resistance against Vibrio alginolyticus

Indian Journal of Animal Research ◽

10.18805/ijar.b-1158 ◽

2020 ◽

Author(s):

A. A. Laith ◽

S. Badr ◽

M. K. Ros-Amira ◽

I. S. Hassan ◽

A. W.M. Effendy ◽

...

Keyword(s):

Oreochromis Niloticus ◽

Lysozyme Activity ◽

Control Group ◽

Perna Viridis ◽

Rrna Gene ◽

Bacterial Strains ◽

Commercial Feed ◽

Microbial Infections ◽

The 16S Rrna Gene

The efficiency of using lactic acid bacteria derived from chicken to be used in fish to limit microbial infections in aquaculture was investigated. Gram-positive isolates were cultured on Man Rogosa Sharp agar (MRS). Identification of bacterial strains was done by analyzing nucleotide sequence of the 16S rRNA gene. Lactobacillus plantarum (98%) was isolated from Oreochromis niloticus and Enterococcus durans (96%) was isolated from Gallus gallus. The sequences were deposited in GenBank with the Accession No. of MF197402 and MF197403, respectively. Experimental mussels were divided into 3 groups; control group fed commercial feed only, Treatment 1 and Treatment 2 were fed with commercial feed supplemented with the candidate probiotics isolated from chicken and fish, respectively, for 21 days. P. viridis were immersed in V. alginolyticus 1.0 ×106 CFU/ml. L. plantarum significantly affected haemocyte count, lysozyme activity and mortality rate, whereas E. durans significantly affect lysozyme activity only.

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Insights into the Oral Bacterial Microbiota of Sows

Microorganisms ◽

10.3390/microorganisms9112314 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2314

Author(s):

Jasmine Hattab ◽

Giuseppe Marruchella ◽

Alberto Pallavicini ◽

Fabrizia Gionechetti ◽

Francesco Mosca ◽

...

Keyword(s):

Oral Fluid ◽

Animal Health ◽

16S Rrna Gene Sequencing ◽

Research Field ◽

Rrna Gene ◽

Bacterial Populations ◽

Bacterial Microbiota ◽

Lactating Sows ◽

Original Contribution ◽

Rrna Gene Sequencing

The investigation of bacterial microbiota represents a developing research field in veterinary medicine intended to look for correlations between animal health and the balance within bacterial populations. The aim of the present work was to define the bacterial microbiota of the oral cavity of healthy sows, which had not been thoroughly described so far. In total, 22 samples of oral fluid were collected and analyzed by 16S-rRNA gene sequencing. CLC Genomics Workbench 20.0 (QIAGEN Digital Insights, Aarhus, Denmark) was then used to examine the results. The predominant orders were Lactobacillales, Clostridiales, and Corynebacteriales. Lactobacillaceae, Corynebacteriaceae, Moraxellaceae, Aerococcaceae, and Staphylococcaceae were the most represented families. As regards the most abundant genera, Lactobacillus, Corynebacterium, Acinetobacter, Staphylococcus, Rothia, Aerococcus, and Clostridium can be pointed out as the bacterial core microbiota. Sows were also divided into “gestating” and “lactating” groups, and mild differences were found between pregnant and lactating sows. The data herein described represent an original contribution to the knowledge of the porcine bacterial microbiota. Moreover, the choice of sows as experimental animals was strategic for identifying the adult microbial community. These data provide a basis for further studies on the oral bacterial microbiota of pigs.

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Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents

Viruses ◽

10.3390/v13122341 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2341

Author(s):

Anna-Ursula Happel ◽

Christina Balle ◽

Brandon S. Maust ◽

Iyaloo N. Konstantinus ◽

Katherine Gill ◽

...

Keyword(s):

South African ◽

Female Genital Tract ◽

Genomic Analysis ◽

Bacterial Strains ◽

Associated Bacteria ◽

Bacterial Microbiota ◽

Metagenome Sequencing ◽

And Function ◽

Female Genital

The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.

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Antifouling activities of extracellular polymeric substances produced by marine bacteria associated with the gastropod (Babylonia sp.)

Nova Biotechnologica et Chimica ◽

10.2478/nbec-2018-0012 ◽

2018 ◽

Vol 17 (2) ◽

pp. 115-124 ◽

Cited By ~ 1

Author(s):

Nadarajan Viju ◽

Nagarajan Ezhilraj ◽

Chellamnadar Vaikundavasagom Sunjai Shankar ◽

Stanislaus Mary Josephine Punitha ◽

Sathianeson Satheesh

Keyword(s):

Extracellular Polymeric Substances ◽

16S Rrna Gene Sequencing ◽

Bioactive Metabolites ◽

Rrna Gene ◽

Bacterial Strains ◽

Ft Ir ◽

Rrna Gene Sequencing

AbstractBacteria associated with surfaces have been frequently cited as a potential source for the isolation of bioactive metabolites. In this study, bacteria associated with marine gastropod, Babylonia sp. were isolated and screened for antibacterial activity against biofilm-forming bacteria. The antibiofilm and antifouling effect of the selected surface- associated bacterial strains were examined under in vitro and in vivo conditions. Results showed that the extracellular polymeric substances (EPS) of the bacterial strain CML associated with gastropod species considerably reduced the adhesion of biofilm-forming bacteria on glass coupons. Besides, the antifouling coat prepared by incorporating of this EPS into polyurethane varnish prevented the settlement of biofoulers on test substratum submerged in marine waters. The functional groups present in the EPS were analyzed using FT-IR. The bacterium responsible for the production of the bioactive EPS was identified as Bacillus subtilis subsp. by 16S rRNA gene sequencing. More detailed characterization of the identified bioactive EPS could lead to the isolation of a novel natural antifouling product.

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DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

Revista Fitotecnia Mexicana ◽

10.35196/rfm.2018.3.255-264 ◽

2018 ◽

Vol 41 (3) ◽

pp. 255-264 ◽

Cited By ~ 1

Author(s):

J. Abraham Pérez-Pérez ◽

David Espinosa-Victoria ◽

Hilda V. Silva-Rojas ◽

Lucía López-Reyes

Keyword(s):

Bacterial Diversity ◽

Digestive Tract ◽

Bacterial Species ◽

Brain Heart Infusion ◽

Rrna Gene ◽

Eisenia Foetida ◽

Bacterial Isolates ◽

Bacterial Microbiota ◽

Decomposition Of Organic Matter ◽

Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

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Campylobacter insulaenigrae bacteremia with meningitis: a case report

BMC Infectious Diseases ◽

10.1186/s12879-021-06353-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Moe Kyotani ◽

Tsuneaki Kenzaka ◽

Hozuka Akita ◽

Soichi Arakawa

Keyword(s):

Blood Culture ◽

Marine Mammals ◽

Chronic Subdural Hematoma ◽

16S Rrna Gene Sequencing ◽

Enhancement Effect ◽

Rrna Gene ◽

Clinical Report ◽

Bacterial Strains ◽

Fisher Syndrome ◽

First Case

Abstract Background The bacterium Campylobacter insulaenigrae was first isolated from marine mammals of Scotland in 2004. Only one case of C. insulaenigrae infection in humans has been previously reported. Case presentation An 89-year-old Japanese man without dementia was admitted to our hospital, because he presented with a fever of 38 °C and weakness in right leg since 5 days. He had organized chronic subdural hematoma (CSH), and no history of pre-infection. At the time of admission, he had paralysis of the extraocular muscle, ataxia, and low manual muscle test score of the right side. He was suspected to have Miller Fisher syndrome; however, these symptoms improved without any treatment. On day 22 in the hospital, the patient presented a fever of 38.8 °C, left cranial nerve disorder, and hemiplegia. On day 25, the patient presented with signs of meningeal irritation; cerebrospinal fluid examination indicated an increase in the number of apocytes and a low glucose level. A contrast magnetic resonance imaging (MRI) scan of the patient’s head indicated a contrast enhancement effect in his right meninges. The blood culture showed presence of spirillums; 16S rRNA gene sequencing confirmed that the spirillums in the blood culture were Campylobacter insulaenigrae (C. insulaenigrae). We started treatment with meropenem for bacteremia and meningitis. When the symptoms improved, meropenem was replaced with ampicillin, based on the result of the drug sensitivity test. The treatment continued for 4 weeks. Conclusions We report the first case of meningitis caused by C. insulaenigrae bacteremia in humans, and the second clinical report of C. insulaenigrae infection in humans. The bacterial strains isolated from humans and marine mammals had different genotypes. This suggests that different genotypes could be responsible for differences in the hosts. Further case studies are needed to establish the reasons behind the difference in the manifestations of C. insulaenigrae infections reported so far.

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Microbiome of Odontogenic Abscesses

Microorganisms ◽

10.3390/microorganisms9061307 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1307

Author(s):

Sebastian Böttger ◽

Silke Zechel-Gran ◽

Daniel Schmermund ◽

Philipp Streckbein ◽

Jan-Falco Wilbrand ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Oral Microbiome ◽

Minor Role ◽

Rrna Gene ◽

Sequencing Analysis ◽

Bacterial Strains ◽

16S Rrna Gene Analysis ◽

Odontogenic Infections ◽

Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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