Microbiota Profile with Stunting Children in West Sumatera Province, Indonesia

BACKGROUND: Microbiota profile plays an important role in the growth of children. Recently, a number of microbiota profile studies have illustrated association with child stunting. AIM: Here, this study applied microbiota profile for stunting children in Indonesia to know a framework for future activities toward further characterization of microbiota profile contribution to stunting. METHODS: In this case–control study, we collected 96 samples with 48 stunting children and 48 non-stunting children in Pasaman and West Pasaman district as stunting locus areas in West Sumatra Province, Indonesia. All study subjects met the inclusion criteria: Children ≤3 years of age and they did not suffer from gastrointestinal disorders. Samples collected were then carried out by intestinal bacterial DNA extraction. All sequences were obtained from the bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a child fecal sample. Bioinformatic analysis of microbiota DNA sequencing results compared with the intestinal microbiota profile of infants. RESULTS: This study found in intestinal of stunting children identified 61 species of bacteria which were only found in the intestines of stunting children and not found in non-stunting children. The dominant bacteria in intestinal microbiota profile of Pasaman and West Pasaman district, West Sumatera Province, Indonesia, among stunting children were Firmicutes (47.52%), Proteobacteria (21.12%), and Bacteroidetes (16.15%). The high number of these microbiota associated with high amount of carbohydrate intake among stunting children than dietary protein. CONCLUSION: This study confirmed the role of microbiota profile in the incidence of stunting children.

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Characterization of biliary microbiota dysbiosis in extrahepatic cholangiocarcinoma

PLoS ONE ◽

10.1371/journal.pone.0247798 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247798

Author(s):

Massa Saab ◽

Denis Mestivier ◽

Masoudreza Sohrabi ◽

Christophe Rodriguez ◽

Mahmood Reza Khonsari ◽

...

Keyword(s):

Endoscopic Retrograde ◽

Extrahepatic Cholangiocarcinoma ◽

Bacterial Dna ◽

Associated Diseases ◽

Digestive Cancers ◽

Rrna Sequencing ◽

Inflammatory Bowel ◽

Bacterial Dna Extraction

Extrahepatic cholangiocarcinoma (CCA) accounts for 3% of digestive cancers. The role of biliary microbiota as an environment-related modulator has been scarcely investigated in CCA, and the putative impact of associated diseases has not been yet assessed. We characterized the biliary microbiota in CCA patients in order to identify a specific CCA-related dysbiosis. The biliary effluents were collected through an endoscopic retrograde pancreatic cholangiography (ERCP) examination involving 28 CCA and 47 patients with gallstones, herein considered as controls. The biliary effluents were submitted to bacterial DNA extraction and 16S rRNA sequencing, using Illumina technology. Overall, 32% of CCA and 22% of controls displayed another associated disease, such as diabetes, pancreatitis, inflammatory bowel disease, or primary sclerosing cholangitis. Such associated diseases were considered in the comparisons that were made. Principal coordinate analysis (PCoA) detected a significant disparity of biliary microbiota composition between CCA patients and controls without an associated disease. Amongst the most abundant phyla, Proteobacteria did not significantly differ between CCA patients and controls, whereas Firmicutes levels were lower and Bacteroidetes higher in CCAs’ biliary microbiota than in the controls’ microbiota. The most abundant genera were Enterococcus, Streptococcus, Bacteroides, Klebsiella, and Pyramidobacter in CCA’s biliary microbiota. Additionally, levels of Bacteroides, Geobacillus, Meiothermus, and Anoxybacillus genera were significantly higher in CCA patients’ biliary microbiota, without an associated disease, in comparison with controls. A specific CCA-related dysbiosis was identified as compared to controls independently from associated diseases. This suggests that a microorganism community may be involved in CCA pathogenesis.

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Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

Egyptian Journal of Biological Pest Control ◽

10.1186/s41938-020-00343-9 ◽

2020 ◽

Vol 30 (1) ◽

Author(s):

Rashid Pervez ◽

Showkat Ahmad Lone ◽

Sasmita Pattnaik

Keyword(s):

Insect Pests ◽

Entomopathogenic Nematode ◽

Alcaligenes Faecalis ◽

Symbiotic Bacteria ◽

Rrna Gene ◽

Main Body ◽

Associated Bacteria ◽

Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

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Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?

Pathogens ◽

10.3390/pathogens10040396 ◽

2021 ◽

Vol 10 (4) ◽

pp. 396

Author(s):

Ewa Sajnaga ◽

Marcin Skowronek ◽

Agnieszka Kalwasińska ◽

Waldemar Kazimierczak ◽

Karolina Ferenc ◽

...

Keyword(s):

Gut Microbiota ◽

Entomopathogenic Nematodes ◽

Bacterial Species ◽

Antagonistic Activity ◽

Rrna Gene ◽

Nanopore Sequencing ◽

Bacterial Phyla ◽

Melolontha Melolontha

This study focused on the potential relationships between midgut microbiota of the common cockchafer Melolontha melolontha larvae and their resistance to entomopathogenic nematodes (EPN) infection. We investigated the bacterial community associated with control and unsusceptible EPN-exposed insects through nanopore sequencing of the 16S rRNA gene. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant bacterial phyla within the complex and variable midgut microbiota of the wild M. melolontha larvae. The core microbiota was found to include 82 genera, which accounted for 3.4% of the total number of identified genera. The EPN-resistant larvae differed significantly from the control ones in the abundance of many genera belonging to the Actinomycetales, Rhizobiales, and Clostridiales orders. Additionally, the analysis of the microbiome networks revealed different sets of keystone midgut bacterial genera between these two groups of insects, indicating differences in the mutual interactions between bacteria. Finally, we detected Xenorhabdus and Photorhabdus as gut residents and various bacterial species exhibiting antagonistic activity against these entomopathogens. This study paves the way to further research aimed at unravelling the role of the host gut microbiota on the output of EPN infection, which may contribute to enhancement of the efficiency of nematodes used in eco-friendly pest management.

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Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa004 ◽

2020 ◽

Vol 96 (2) ◽

Author(s):

Yu-Xi Zhu ◽

Zhang-Rong Song ◽

Shi-Mei Huo ◽

Kun Yang ◽

Xiao-Yue Hong

Keyword(s):

Spider Mite ◽

Potential Role ◽

Developmental Stages ◽

Spider Mites ◽

Rrna Gene ◽

Associated Bacteria ◽

Operational Taxonomic Units ◽

Dominant Bacteria ◽

The 16S Rrna Gene

ABSTRACT Most arthropod-associated bacterial communities play a crucial role in host functional traits, whose structure could be dominated by endosymbionts. The spider mite Tetranychus truncatus is a notorious agricultural pest harboring various endosymbionts, yet the effects of endosymbionts on spider mite microbiota remain largely unknown. Here, using deep sequencing of the 16S rRNA gene, we characterized the microbiota of male and female T. truncatus with different endosymbionts (Wolbachia and Spiroplasma) across different developmental stages. Although the spider mite microbiota composition varied across the different developmental stages, Proteobacteria were the most dominant bacteria harbored in all samples. Positive relationships among related operational taxonomic units dominated the significant coassociation networks among bacteria. Moreover, the spider mites coinfected with Wolbachia and Spiroplasma had a significantly higher daily fecundity and juvenile survival rate than the singly infected or uninfected spider mites. The possible function of spider-mite associated bacteria was discussed. Our results highlight the dynamics of spider mite microbiotas across different life stages, and the potential role of endosymbionts in shaping the microbiota of spider mites and improving host fitness.

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Characterization of bacterial communities of rhizosphere and rhizoplane of Early Zhukovsky potato

E3S Web of Conferences ◽

10.1051/e3sconf/202022202050 ◽

2020 ◽

Vol 222 ◽

pp. 02050

Author(s):

Marat Lutfulin ◽

Darya Zaripova ◽

Oksana Moiseeva ◽

Semen Vologin ◽

Ayslu Mardanova

Keyword(s):

Bacterial Communities ◽

Functional Role ◽

Agricultural Crop ◽

Potato Root ◽

Bacterial Microbiota ◽

16S R Rna ◽

Significant Difference ◽

Dominant Bacteria

Identification of patterns of formation of bacterial communities of the rhizosphere and rhizoplane of potato (Solanum tuberosum L.), the most important agricultural crop, is necessary for the introduction and maintenance of sustainable organic farming. The purpose of this work was the study of the biodiversity of the bacterial microbiota of the rhizosphere and rhizoplane of Early Zhukovsky potato, cultivated on gray forest soils. Comparative analysis based on sequencing of the 16S R RNA gene showed a significant difference in the representation of different groups of bacteria in these potato root compartments. Thus, the proportions of the dominant bacteria in the rhizosphere and rhizoplane of the Proteobacteria phylum reach 47.66% ± 7.22 % and 86.35 % ± 0.53%, respectively (P < 0.05). In contrast, the representation of phylum Bacteroidetes and Firmicutes in the rhizosphere is significantly higher and reaches 41.45 % ± 10.42% and 6.49 % ± 3.23%, respectively, compared to the rhizoplane (7.84 % ± 1.24 % and 0.43 % ± 0.48 %, (P < 0.05). At the same time, Actinobacteria phylum bacteria are present in both compartments in approximately equal amounts (4.40 % ± 1.81% in the rhizosphere and 5.37 % ± 1.42% in the rhizoplane). Thus, it was found that potato forms different bacterial communities in the rhizosphere and rhizoplane in quantitative proportions, which is probably determined by the functional role of these microorganisms in the plant physiology.

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Identification and Characterization of Two Bordetella avium Gene Products Required for Hemagglutination

Infection and Immunity ◽

10.1128/iai.00140-10 ◽

2010 ◽

Vol 78 (6) ◽

pp. 2370-2376 ◽

Cited By ~ 14

Author(s):

Louise M. Temple ◽

David M. Miyamoto ◽

Manju Mehta ◽

Christian M. Capitini ◽

Stephen Von Stetina ◽

...

Keyword(s):

Whooping Cough ◽

Bioinformatic Analysis ◽

Tracheal Ring ◽

Tracheal Cell ◽

Bordetella Avium ◽

Identification And Characterization

ABSTRACT Bordetella avium causes bordetellosis in birds, a disease similar to whooping cough caused by Bordetella pertussis in children. B. avium agglutinates guinea pig erythrocytes via an unknown mechanism. Loss of hemagglutination ability results in attenuation. We report the use of transposon mutagenesis to identify two genes required for hemagglutination. The genes (hagA and hagB) were adjacent and divergently oriented and had no orthologs in the genomes of other Bordetella species. Construction of in-frame, unmarked mutations in each gene allowed examination of the role of each in conferring erythrocyte agglutination, explanted tracheal cell adherence, and turkey poult tracheal colonization. In all of the in vitro and in vivo assays, the requirement for the trans-acting products of hagA and hagB (HagA and HagB) was readily shown. Western blotting, using antibodies to purified HagA and HagB, revealed proteins of the predicted sizes of HagA and HagB in an outer membrane-enriched fraction. Antiserum to HagB, but not HagA, blocked B. avium erythrocyte agglutination and explanted turkey tracheal ring binding. Bioinformatic analysis indicated the similarity of HagA and HagB to several two-component secretory apparatuses in which one product facilitates the exposition of the other. HagB has the potential to serve as a useful immunogen to protect turkeys against colonization and subsequent disease.

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Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls

Journal of Medical Microbiology ◽

10.1099/jmm.0.007302-0 ◽

2009 ◽

Vol 58 (4) ◽

pp. 509-516 ◽

Cited By ~ 156

Author(s):

Johan Dicksved ◽

Mathilda Lindberg ◽

Magnus Rosenquist ◽

Helena Enroth ◽

Janet K. Jansson ◽

...

Keyword(s):

Gastric Cancer ◽

Gastric Acid ◽

Rflp Analysis ◽

Rrna Gene ◽

Bacterial Phyla ◽

Increased Risk ◽

H Pylori ◽

Development Of Gastric Cancer

Persistent infection of the gastric mucosa by Helicobacter pylori can initiate an inflammatory cascade that progresses into atrophic gastritis, a condition associated with reduced capacity for secretion of gastric acid and an increased risk of developing gastric cancer. The role of H. pylori as an initiator of inflammation is evident but the mechanism for development into gastric cancer has not yet been proven. A reduced capacity for gastric acid secretion allows survival and proliferation of other microbes that normally are killed by the acidic environment. It has been postulated that some of these species may be involved in the development of gastric cancer; however, their identities are poorly defined. In this study, the gastric microbiota from ten patients with gastric cancer was characterized and compared with that from five dyspeptic controls using the molecular profiling approach terminal restriction fragment length polymorphism (T-RFLP), in combination with 16S rRNA gene cloning and sequencing. T-RFLP analysis revealed a complex bacterial community in the cancer patients that was not significantly different from that in the controls. Sequencing of 140 clones revealed 102 phylotypes, with representatives from five bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria). The data revealed a relatively low abundance of H. pylori and showed that the gastric cancer microbiota was instead dominated by different species of the genera Streptococcus, Lactobacillus, Veillonella and Prevotella. The respective role of these species in development of gastric cancer remains to be determined.

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Culex pipiens and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues

Parasites & Vectors ◽

10.1186/s13071-020-04408-4 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Elijah O. Juma ◽

Chang-Hyun Kim ◽

Christopher Dunlap ◽

Brian F. Allan ◽

Chris M. Stone

Keyword(s):

Bacterial Communities ◽

Culex Pipiens ◽

Mosquito Species ◽

Gravid Female ◽

Distance Matrix ◽

Rrna Gene ◽

Culex Restuans ◽

Host Tissues

Abstract Background The bacterial communities associated with mosquito eggs are an essential component of the mosquito microbiota, yet there are few studies characterizing and comparing the microbiota of mosquito eggs to other host tissues. Methods We sampled gravid female Culex pipiens L. and Culex restuans Theobald from the field, allowed them to oviposit in the laboratory, and characterized the bacterial communities associated with their egg rafts and midguts for comparison through MiSeq sequencing of the 16S rRNA gene. Results Bacterial richness was higher in egg rafts than in midguts for both species, and higher in Cx pipiens than Cx. restuans. The midgut samples of Cx. pipiens and Cx. restuans were dominated by Providencia. Culex pipiens and Cx. restuans egg rafts samples were dominated by Ralstonia and Novosphingobium, respectively. NMDS ordination based on Bray-Curtis distance matrix revealed that egg-raft samples, or midgut tissues harbored similar bacterial communities regardless of the mosquito species. Within each mosquito species, there was a distinct clustering of bacterial communities between egg raft and midgut tissues. Conclusion These findings expand the list of described bacterial communities associated with Cx. pipiens and Cx. restuans and the additional characterization of the egg raft bacterial communities facilitates comparative analysis of mosquito host tissues, providing a basis for future studies seeking to understand any functional role of the bacterial communities in mosquito biology.

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Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145

BioMed Research International ◽

10.1155/2017/9529501 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Olga Tsypik ◽

Roman Makitrynskyy ◽

Agnieszka Bera ◽

Lijiang Song ◽

Wolfgang Wohlleben ◽

...

Keyword(s):

Antibiotic Production ◽

Streptomyces Coelicolor ◽

Regulatory Gene ◽

Functional Characterization ◽

Bioinformatic Analysis ◽

Transcriptional Analysis ◽

Dependent Manner ◽

Putative Operon

Here we report functional characterization of the Streptomyces coelicolor M145 gene SCO1678, which encodes a GntR-like regulator of the FadR subfamily. Bioinformatic analysis suggested that SCO1678 is part of putative operon (gnt) involved in gluconate metabolism. Combining the results of SCO1678 knockout, transcriptional analysis of gnt operon, and Sco1678 protein-DNA electromobility shift assays, we established that Sco1678 protein controls the gluconate operon. It does so via repression of its transcription from a single promoter located between genes SCO1678 and SCO1679. The knockout also influenced, in a medium-dependent manner, the production of secondary metabolites by S. coelicolor. In comparison to the wild type, on gluconate-containing minimal medium, the SCO1678 mutant produced much less actinorhodin and accumulated a yellow-colored pigment, likely to be the cryptic polyketide coelimycin. Possible links between gluconate metabolism and antibiotic production are discussed.

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Culex pipiens L. and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues

10.1101/2020.05.23.112128 ◽

2020 ◽

Author(s):

Elijah O. Juma ◽

Chang-Hyun Kim ◽

Christopher Dunlap ◽

Brian F. Allan ◽

Chris M. Stone

Keyword(s):

Bacterial Communities ◽

Culex Pipiens ◽

Mosquito Species ◽

Gravid Female ◽

Distance Matrix ◽

Rrna Gene ◽

Culex Restuans ◽

Host Tissues

AbstractBackgroundThe bacterial communities associated with mosquito eggs are an essential component of the mosquito microbiota, yet there are few studies characterizing and comparing the microbiota of mosquito eggs to other host tissues.MethodsWe sampled gravid female Culex pipiens and Culex restuans from the field, allowed them to oviposit in the laboratory, and characterized the microbiota associated with their egg rafts and midguts for comparison through MiSeq sequencing of the 16S rRNA gene.ResultsBacterial richness was higher in egg rafts than in midguts for both species, and higher in Cx pipiens L. than Cx. restuans. The midgut samples of Cx. pipiens and Cx. restuans were dominated by Providencia. Culex pipiens L. and Cx. restuans egg rafts samples were dominated by Ralstonia and Novosphingobium, respectively. NMDS ordination based on Bray-Curtis distance matrix revealed that egg raft samples, or midgut tissues harbored similar bacterial communities regardless of the mosquito species. Within each mosquito species, there were distinct clustering of bacterial communities between egg raft and midgut tissues.ConclusionThese findings expand the list of described bacterial communities associated with Cx. pipiens L. and Cx. restuans and the additional characterization of the egg raft bacterial communities facilitates comparative analysis of mosquito host tissues, providing a basis for future studies seeking to understand any functional role of microbiota in mosquito biology.

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