scholarly journals Gene–Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism

2021 ◽  
Vol 9 (5) ◽  
pp. 883
Author(s):  
Shijie Liu ◽  
Zhifeng Fang ◽  
Hongchao Wang ◽  
Qixiao Zhai ◽  
Feng Hang ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Carbon Sources ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Strain Specificity ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Species ◽  
Large Gene ◽  
Wide Range ◽  
Almost All

Bifidobacteria are among the first colonizers of the human gastrointestinal tract. Different bacterial species use different mechanisms for utilization of various carbon sources in order to establish themselves in the complex microbial ecosystem of the gut. However, these mechanisms still need to be explored. Here, a large gene–phenotype correlation analysis was carried out to explore the metabolic and genetic diversity of bifidobacterial carbohydrate utilization abilities. In this study, we used 21 different carbohydrates to determine the growth phenotypes, the distribution of glycoside hydrolases (GHs), and gene clusters related to the utilization of multiple carbon sources in six human-residential Bifidobacterium species. Five carbohydrates significantly stimulated growth of almost all strains, while the remaining sugars exhibited species- and strain-specificity. Correspondingly, different Bifidobacterium species also had specific GHs involved in fermentation of plant or host glycans. Moreover, we analyzed several carbohydrate utilization gene clusters, such as 2-fucosyllactose (2′FL), sialic acid (SA), and fructooligosaccharide (FOS). In summary, by using 217 bifidobacterial strains and a wide range of growth substrates, our research revealed inter- and intra-species differences in bifidobacterial in terms of carbohydrate utilization. The findings of this study are useful for the process of developing prebiotics for optimum growth of probiotics, especially Bifidobacterium species.

scholarly journals Additional Og-Typing PCR Techniques Targeting Escherichia coli-Novel and Shigella-Unique O-Antigen Biosynthesis Gene Clusters

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Atsushi Iguchi ◽  
Hironobu Nishii ◽  
Kazuko Seto ◽  
Jiro Mitobe ◽  
Kenichi Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Strong Association ◽  
Gene Clusters ◽  
Epidemiological Studies ◽  
Content Type ◽  
E Coli ◽  
O Antigen ◽  
Wide Range ◽  
Biosynthesis Gene ◽  
Almost All

ABSTRACT The O-serogrouping of pathogenic Escherichia coli is a standard method for subtyping strains for epidemiological studies and controls. O-serogroup diversification shows a strong association with the genetic diversity in some O-antigen biosynthesis gene clusters. Through genomic studies, in addition to the types of O-antigen biosynthesis gene clusters (Og-types) from conventional O-serogroup strains, a number of novel Og-types have been found in E. coli isolates. To assist outbreak investigations and surveillance of pathogenic E. coli at inspection institutes, in previous studies, we developed PCR methods that could determine almost all conventional O-serogroups and some novel Og-types. However, there are still many Og-types that may not be determined by simple genetic methods such as PCR. Thus, in the present study, we aimed to develop an additional Og-typing PCR system. Based on the novel Og-types, including OgN32, OgN33, and OgN34, presented in this study, we designed an additional 24 PCR primer pairs targeting 14 novel and 2 diversified E. coli Og-types and 8 Shigella-unique Og-types. Subsequently, we developed 5 new multiplex PCR sets consisting of 33 primers, including the aforementioned 24 primers and 9 primers reported in previous studies. The accuracy and specificity of the PCR system was validated using approximately 260 E. coli and Shigella O-serogroup and Og-type reference strains. The Og-typing PCR system reported here can determine a wide range of Og-types of E. coli and may help epidemiological studies, in addition to the surveillance of pathogenic E. coli.

scholarly journals Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Yuki Saito ◽  
Akira Shigehisa ◽  
Yohei Watanabe ◽  
Naoki Tsukuda ◽  
Kaoru Moriyama-Ohara ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Adolescentis ◽  
Content Type

ABSTRACT Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

scholarly journals Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

2015 ◽  
Vol 81 (16) ◽  
pp. 5458-5470 ◽  
Author(s):  
Corina Ceapa ◽  
Jolanda Lambert ◽  
Kees van Limpt ◽  
Michiel Wels ◽  
Tamara Smokvina ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Bacterial Species ◽  
Draft Genome ◽  
Carbon Sources ◽  
Lactobacillus Rhamnosus ◽  
Genotypic Diversity ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Healthy Humans ◽  
Niche Adaptation

ABSTRACTLactobacillus rhamnosusis a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains ofL. rhamnosusin relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65L. rhamnosusstrains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification ofL. rhamnosusstrains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes ofL. rhamnosusGG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters:l-rhamnose, cellobiose,l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate withl-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the speciesL. rhamnosusand explores the relationships between specific carbohydrate utilization capacities and genotype and/or niche adaptation of this species.

scholarly journals Ethanolamine Utilization Contributes to Proliferation ofSalmonella entericaSerovar Typhimurium in Food and in Nematodes

2010 ◽  
Vol 77 (1) ◽  
pp. 281-290 ◽  
Author(s):  
Shabarinath Srikumar ◽  
Thilo M. Fuchs
Keyword(s):  
Salmonella Enterica ◽  
De Novo ◽  
Bacterial Species ◽  
Gene Activation ◽  
Carbon Sources ◽  
Egg Yolk ◽  
Gene Clusters ◽  
Luciferase Reporter ◽  
Infection Model ◽  
Reporter System

ABSTRACTOnly three pathogenic bacterial species,Salmonella enterica,Clostridium perfringens, andListeria monocytogenes, are able to utilize both ethanolamine and 1,2-propanediol as a sole carbon source. Degradation of these substrates, abundant in food and the gut, depends on cobalamin, which is synthesizedde novoonly under anaerobic conditions. Although theeut,pdu, andcob-cbigene clusters comprise 40 kb, the conditions under which they confer a selection advantage on these food-borne pathogens remain largely unknown. Here we used the luciferase reporter system to determine the response of theSalmonella entericaserovar Typhimurium promoters PeutS, PpocR, PpduF, and PpduAto a set of carbon sources, to egg yolk, to whole milk, and to milk protein or fat fractions. Depending on the supplements, specific inductions up to 3 orders of magnitude were observed for PeutSand PpduA, which drive the expression of mosteutandpdugenes. To correlate these significant expression data with growth properties, nonpolar deletions ofpocR, regulating thepduandcob-cbigenes, and ofeutR, involved ineutgene activation, were constructed inS. Typhimurium strain 14028. During exponential growth of the mutants 14028ΔpocRand 14028ΔeutR, 2- to 3-fold-reduced proliferation in milk and egg yolk was observed. Using theCaenorhabditis elegansinfection model, we could also demonstrate that the proliferation ofS. Typhimurium in the nematode is supported by an active ethanolamine degradation pathway. Taking these findings together, this study quantifies the differential expression ofeutandpdugenes under distinct conditions and provides experimental evidence that the ethanolamine utilization pathway allows salmonellae to occupy specific metabolic niches within food environments and within their host organisms.

scholarly journals Genomic insight into pathogenicity of dematiaceous fungusCorynespora cassiicola

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2841 ◽  
Author(s):  
Hong Keat Looi ◽  
Yue Fen Toh ◽  
Su Mei Yew ◽  
Shiang Ling Na ◽  
Yung-Chie Tan ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Fungal Genome ◽  
Leaf Spot Disease ◽  
Cell Wall Degrading Enzymes ◽  
Pathogenic Potential ◽  
Dematiaceous Fungus ◽  
Wide Range ◽  
Biosynthesis Gene ◽  
Carbohydrate Esterases

Corynespora cassiicolais a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient’s contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore,ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.

scholarly journals Isolation and Characterization of Chickpea (Cicer arietinum L.) Nodulating Rhizobia Collected from South Wollo Zone, Ethiopia

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Gedefaw Wubie ◽  
Mussa Adal
Keyword(s):  
Nitrogen Source ◽  
Carbon Sources ◽  
Dry Weight ◽  
Maximum Temperature ◽  
High Concentration ◽  
Carbohydrate Utilization ◽  
Shoot Dry Weight ◽  
Isolation And Characterization ◽  
Almost All

This study aimed at screening rhizobial isolates of chickpea and evaluating their symbiotic nitrogen fixation efficiency and tolerance to abiotic stresses. A total of 107 (100%) isolates were collected of which 52 (48.6%) were confirmed as chickpea rhizobia using preliminary tests. Among 52 (48.6%) isolates, 46 (88.5%) have induced nodulation on chickpea under greenhouse and were screened under in vitro conditions and 6 (11.5%) of them were discarded due to fail to nodulate. The greenhouse data showed the highest nodule number (68.67 plant−1), nodule dry weight (0.17 g plant−1), and shoot dry weight (0.81 g plant−1) were scored by plants inoculated with isolates WUCR 17, WUCR 1, and WUCR 66, respectively. Among authenticated isolates, 73.9%, 21.7%, and 4.3% were highly effective, effective, and lowly effective, respectively. The physiological test showed 15% of isolates tolerated 13% salt concentration and 10.9% of isolates grew at pH 4–10 range. All isolates grew at 20–35°C and 13% grew at maximum temperature (50°C). The isolates showed better resistance to the tested antibiotics at low concentration (2.5 μg/ml) but the majorities were sensitive at high concentration (10 μg/ml). Among the isolates, 13% tolerated all tested heavy metals but 48% were sensitive to mercury. Regarding the carbohydrate utilization test, 52.2% catabolized all the tested 11 carbon sources but 6.5% of them utilized only 63.6% carbon sources. Amino acid utilization showed isolates (85%) utilized D-alanine except WUCR (14, 25, 31, 34, 39, 59, and 76) and 76% of the isolates utilized arginine and phenylalanine and 74% utilized leucine as a nitrogen source. Of the isolates, 43.5% of them utilized both D-alanine and arginine as a nitrogen source. In almost all tests conducted, isolates WUCR 1 and 5 performed top and were recommended as potential candidates for microbial inoculants.

scholarly journals Description of Schaedlerella arabinophila gen. nov., sp. nov., a D-arabinose utilizing bacterium isolated from feces of C57BL/6J mice and a close relative of Clostridium sp. ASF 502

2018 ◽  
Author(s):  
Melissa Soh ◽  
Sou Miyake ◽  
Austin Lim ◽  
Henning Seedorf
Keyword(s):  
Bacterial Species ◽  
Carbon Sources ◽  
Genomic Analysis ◽  
Close Relative ◽  
Rrna Gene ◽  
Gene Repertoire ◽  
Large Gene ◽  
Technological Advances ◽  
Genome Content ◽  
Genome Analyses

The use of gnotobiotics has gained large interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotics mouse model, the Altered Schaedler Flora (ASF) has been used for several decades. ASF comprises eight different bacterial species, which have been characterized to different extent, but only few are available through public strain collections. Here, the isolation of a close relative to one of the less studied ASF strains, Clostridium sp. ASF 502, is reported. Isolate TLL-A1, which shares 99.6% 16S rRNA gene sequence identity with Clostridium sp. ASF 502, was obtained from feces of C57BL/6J mice where is was detectable at a relative abundance of less than one percent. D-arabinose was used as sole carbon source in the anaerobic cultivation medium. Growth experiments with TLL-A1 on different carbon sources and analysis of its ~6.5 gigabase genome indicate that TLL-A1 harbors a large gene repertoire to utilize different carbohydrates for growth. Comparative genome analyses of TLL-A1 and Clostridium sp. ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate activating enzymes. Based on physiology and genomic analysis it is proposed to name TLL-A1 to gen. nov. sp. nov Schaedlerella arabinophila TLL-A1 (DSMZ 106076T; KCTC 15657T). The closely related Clostridium sp. ASF 502 is proposed to be renamed to Schaedlerella arabinophila to reflect its taxonomic standing and to keep 'ASF 502' as strain designation.

scholarly journals Obligate cross-feeding expands the metabolic niche of bacteria

2020 ◽  
Author(s):  
Leonardo Oña ◽  
Samir Giri ◽  
Neele Avermann ◽  
Maximilian Kreienbaum ◽  
Kai M. Thormann ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Phylogenetic Distance ◽  
Niche Space ◽  
Bacterial Populations ◽  
Widespread Occurrence ◽  
Wide Range ◽  
Interaction Partners ◽  
Bacterial Genotypes

AbstractBacteria frequently engage in obligate metabolic mutualisms with other microorganisms. However, it remains generally unclear how the resulting metabolic dependencies affect the ecological niche space accessible to the whole consortium relative to the niche space available to its constituent individuals. Here we address this issue by systematically cultivating metabolically dependent strains of different bacterial species either individually or as pairwise coculture in a wide range of carbon sources. Our results show that obligate cross-feeding is significantly more likely to expand the metabolic niche space of interacting bacterial populations than to contract it. Moreover, niche expansion occurred predominantly between two specialist taxa and correlated positively with the phylogenetic distance between interaction partners. Together, our results demonstrate that obligate cross-feeding can significantly expand the ecological niche space of interacting bacterial genotypes, thus explaining the widespread occurrence of this type of ecological interaction in natural microbiomes.

scholarly journals Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis

2015 ◽  
Vol 112 (10) ◽  
pp. 3086-3091 ◽  
Author(s):  
Rachel Bleich ◽  
Jeramie D. Watrous ◽  
Pieter C. Dorrestein ◽  
Albert A. Bowers ◽  
Elizabeth A. Shank
Keyword(s):  
Natural Products ◽  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Bacterial Species ◽  
Imaging Mass Spectrometry ◽  
Gene Clusters ◽  
Peptide Antibiotics ◽  
Wide Range ◽  
Thiopeptide Antibiotics ◽  
Peptide Gene

Bacteria have evolved the ability to produce a wide range of structurally complex natural products historically called “secondary” metabolites. Although some of these compounds have been identified as bacterial communication cues, more frequently natural products are scrutinized for antibiotic activities that are relevant to human health. However, there has been little regard for how these compounds might otherwise impact the physiology of neighboring microbes present in complex communities. Bacillus cereus secretes molecules that activate expression of biofilm genes in Bacillus subtilis. Here, we use imaging mass spectrometry to identify the thiocillins, a group of thiazolyl peptide antibiotics, as biofilm matrix-inducing compounds produced by B. cereus. We found that thiocillin increased the population of matrix-producing B. subtilis cells and that this activity could be abolished by multiple structural alterations. Importantly, a mutation that eliminated thiocillin’s antibiotic activity did not affect its ability to induce biofilm gene expression in B. subtilis. We go on to show that biofilm induction appears to be a general phenomenon of multiple structurally diverse thiazolyl peptides and use this activity to confirm the presence of thiazolyl peptide gene clusters in other bacterial species. Our results indicate that the roles of secondary metabolites initially identified as antibiotics may have more complex effects—acting not only as killing agents, but also as specific modulators of microbial cellular phenotypes.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

2020 ◽  
Vol 20 ◽  
Author(s):  
Rami Obeid ◽  
Elias Wehbe ◽  
Mohamad Rima ◽  
Mohammad Kabara ◽  
Romeo Al Bersaoui ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Viral Genome ◽  
Virus Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Virus Family ◽  
Crop Fields ◽  
Wide Range ◽  
Almost All ◽  
Das Elisa

Background: Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particularly tobacco, causing a production loss. Objectives: Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. Methods: Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crops samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. Results and Discussion: PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. Conclusion: Our study is the first in Lebanon revealing TMV infection in crop fields, and highlighting the danger that may affect the future of agriculture.

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