scholarly journals Genotyping and plant-derived glycan utilization analysis of Bifidobacterium strains from mother-infant pairs

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zeyu Kan ◽  
Baolong Luo ◽  
Jingjing Cai ◽  
Yan Zhang ◽  
Fengwei Tian ◽  
...  
Keyword(s):  
Bifidobacterium Longum ◽  
Carbon Sources ◽  
Selective Adaptation ◽  
Exact Expression ◽  
Adult Type ◽  
Carbohydrate Utilization ◽  
Intestinal Environment ◽  
Breastfed Infants ◽  
Hydrolysis Of ◽  
Type Strains

Abstract Background Bifidobacteria are important probiotics; some of the beneficial effects of bifidobacteria are achieved by the hydrolysis of glycans in the human gut. However, because the diet of breastfed infants typically lacks plant-derived glycans, in the gut environment of mothers and their breastfed infants, the mother will intake a variety of plant-derived glycans, such as from onions and bananas, through her diet. Under this assumption, we are interested in whether the same species of bifidobacteria isolated from mother-infant pairs present a distinction in their hydrolysis of plant-derived carbohydrates. Results Among the 36 Bifidobacterium strains, bifidobacterial carbohydrate utilization showed two trends related to the intestinal environment where the bacteria lived. Compared with infant-type bifidobacterial strains, adult-type bifidobacterial strains preferred to use plant-derived glycans. Of these strains, 10 isolates, 2 Bifidobacterium pseudocatenulatum (B. pseudocatenulatum), 2 Bifidobacterium pseudolongum (B. pseudolongum), 2 Bifidobacterium bifidum (B. bifidum), 2 Bifidobacterium breve (B. breve), and 2 Bifidobacterium longum (B. longum), were shared between the mother-infant pairs. Moreover, the repetitive sequence-based polymerase chain reaction (rep-PCR) results illustrated that B. pseudolongum and B. bifidum showed genotypic similarities of 95.3 and 98.2%, respectively. Combined with the carbohydrate fermentation study, these results indicated that the adult-type strains have a stronger ability to use plant-derived glycans than infant-type strains. Our work suggests that bifidobacterial carbohydrate metabolism differences resulted in the selective adaptation to the distinct intestinal environment of an adult or breastfed infant. Conclusions The present study revealed that the different gut environments can lead to the differences in the polysaccharide utilization in the same strains of bifidobacterial strains, suggesting a further goal of investigating the exact expression of certain enzymes in response to specific carbon sources.

Lysozyme in breast milk is a selection factor for bifidobacterial colonisation in the infant intestine

2016 ◽  
Vol 7 (1) ◽  
pp. 53-60 ◽  
Author(s):  
J. Minami ◽  
T. Odamaki ◽  
N. Hashikura ◽  
F. Abe ◽  
J.Z. Xiao
Keyword(s):  
Breast Milk ◽  
Bifidobacterium Longum ◽  
Egg White ◽  
Human Breast Milk ◽  
Adult Type ◽  
Residential Characteristics ◽  
High Concentrations ◽  
Different Strains ◽  
Type Strains ◽  
Selection Factor

The objective of this work was to study the residential characteristics of bifidobacteria, which can be classified as either human-residential bifidobacteria (HRB) or non-HRB. We investigated the growth of different strains of HRB and non-HRB in human breast milk with the aim of understanding the mechanisms involved in the unique habitation of each taxon. The growth of 37 strains of different bifidobacterial species or subspecies in breast milk was investigated by incubating each under anaerobic conditions at 37 °C. The tolerance of each strain to either egg white or human lysozyme was compared. Among the infant-type HRB strains, all strains of Bifidobacterium longum subsp. infantis and Bifidobacterium breve grew well in breast milk, but the growth characteristics of B. longum subsp. longum and B. bifidum were strain-dependent. In contrast, the tested strains of adult-type HRB and non-HRB generally failed to grow and died after incubation in breast milk. Most infant-type HRB strains were tolerant to high concentrations of lysozyme, while adult-type HRB strains possessed intermediate tolerance to lysozyme, and non-HRB strains were susceptible to lysozymes of egg white or human origin. These data suggest that breast milk lysozyme content plays a central role in the exclusion of non-HRB, while other factors, together with lysozyme content, are involved in the growth inhibition of adult-type strains in human milk. Our results suggest that infant-type HRB strains would be suitable candidates for use as infant probiotics.

Development of mutants of Gliocladium virens tolerant to benomyl

1990 ◽  
Vol 36 (7) ◽  
pp. 484-489 ◽  
Author(s):  
G. C. Papavizas ◽  
D. P. Roberts ◽  
K. K. Kim
Keyword(s):  
Carbon Source ◽  
Type Strain ◽  
Wild Type Strain ◽  
Carbon Sources ◽  
Sclerotium Rolfsii ◽  
Wild Type ◽  
Gliocladium Virens ◽  
Rhizosphere Competence ◽  
Filter Paper Cellulase ◽  
Type Strains

Aqueous suspensions of conidia of Gliocladium virens strains Gl-3 and Gl-21 were exposed to both ultraviolet radiation and ethyl methanesulfonate. Two mutants of Gl-3 and three of Gl-21 were selected for tolerance to benomyl at 10 μg∙mL−1, as indicated by growth and conidial germination on benomyl-amended potato dextrose agar. The mutants differed considerably from their respective wild-type strains in appearance, growth habit, sporulation, carbon-source utilization, and enzyme activity profiles. Of 10 carbon sources tested, cellobiose, xylose, and xylan were the best for growth, galactose and glucose were intermediate, and arabinose, ribose, and rhamnose were poor sources of carbon. The wild-type strains and the mutants did not utilize cellulose as the sole carbon source for growth. Two benomyl-tolerant mutants of Gl-3 produced less cellulase (β-1,4-glucosidase, carboxymethylcellulase, filter-paper cellulase) than Gl-3. In contrast, mutants of Gl-21 produced more cellulase than the wild-type strain. Only Gl-3 provided control of blight on snapbean caused by Sclerotium rolfsii. Wild-type strain Gl-21 and all mutants from both strains were ineffective biocontrol agents. Key words: Gliocladium, benomyl tolerance, Sclerotium, rhizosphere competence.

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

scholarly journals Effect of Bifidobacterium longum BB536 Administration on the Intestinal Environment, Defecation Frequency and Fecal Characteristics of Human Volunteers

1997 ◽  
Vol 16 (2) ◽  
pp. 53-58 ◽  
Author(s):  
Tomohiro OGATA ◽  
Teiichi NAKAMURA ◽  
Katsue ANJITSU ◽  
Tomoko YAESHIMA ◽  
Sachiko TAKAHASHI ◽  
...  
Keyword(s):  
Bifidobacterium Longum ◽  
Intestinal Environment ◽  
Human Volunteers ◽  
Defecation Frequency

scholarly journals Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

2020 ◽  
Vol 8 (9) ◽  
pp. 1412
Author(s):  
Minji Kim ◽  
In-Tae Cha ◽  
Ki-Eun Lee ◽  
Eun-Young Lee ◽  
Soo-Je Park
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Extracellular Enzymes ◽  
Marine Invertebrates ◽  
Carbon Sources ◽  
Marine Environments ◽  
Metabolic Potential ◽  
Carbohydrate Utilization ◽  
Genes Encoding ◽  
Metagenomic Study

Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

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.

Co-digestion of primary sewage sludge and industrial wastewater under anaerobic sulphate reducing conditions: enzymatic profiles in a recycling sludge bed reactor

2003 ◽  
Vol 48 (4) ◽  
pp. 129-138 ◽  
Author(s):  
C.G. Whiteley ◽  
G. Enongene ◽  
B.I. Pletschke ◽  
P. Rose ◽  
K. Whittington-Jones
Keyword(s):  
Sewage Sludge ◽  
Extracellular Enzymes ◽  
Carbon Sources ◽  
Reduction Process ◽  
Sulphate Reduction ◽  
Ph Profile ◽  
Reducing Conditions ◽  
Sulphide Concentration ◽  
Complex Carbon ◽  
Hydrolysis Of

The first stage in the degradation and recycling of primary sewage sludge and particulate organic matter is the solubilisation and enhanced hydrolysis of complex polymeric organic carbon structures associated with the anaerobic sulphidogenic environment. Solubilization of complex carbon substrates provides the primary reaction in the BioSURE Process, and is effected in the recycling sludge bed reactor (RSBR). During the process of anaerobic digestion, macromolecules are broken down into simpler low molecular weight compounds in the presence of extracellular enzymes. Though hydrolysis of the complex carbon sources was enhanced under biosulphidogenic conditions, no studies have examined the role of enzymes and the enzymatic profiles in the RSBR. To investigate the overall enzymology in the RSBR variations in COD, pH, sulphate, sulphite and sulphide concentrations, carbohydrates, protein and activities of glucosidases, proteases and lipases were studied over 50 days in the reactor at three different depths: 0-16 cm; 16-32 cm; 32-50 cm. While the pH profile remained fairly constant between 6.9 and 7.3 the sulphate and sulphide levels, as expected, changed dramatically as sulphate reduction took place. Proteases, lipases and glucosidases all showed enhanced activity with depth in the bioreactor. It is suggested that the increased sulphide concentration generated during the sulphate reduction process stimulates the enzymes, leading to enhanced solubilisation of primary sewage sludge.

scholarly journals Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

mSphere ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Steven A. Frese ◽  
Andra A. Hutton ◽  
Lindsey N. Contreras ◽  
Claire A. Shaw ◽  
Michelle C. Palumbo ◽  
...  
Keyword(s):  
Human Milk ◽  
Gut Microbiome ◽  
Bifidobacterium Longum ◽  
Specific Substrate ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
Breastfed Infants ◽  
Gut Function ◽  
First Time

ABSTRACT The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function. Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32). Fecal samples were collected during the first 60 postnatal days in both groups. Fecal samples were assessed by 16S rRNA gene sequencing, quantitative PCR, mass spectrometry, and endotoxin measurement. B. infantis-fed infants had significantly higher populations of fecal Bifidobacteriaceae, in particular B. infantis, while EVC001 was fed, and this difference persisted more than 30 days after EVC001 supplementation ceased. Fecal milk oligosaccharides were significantly lower in B. infantis EVC001-fed infants, demonstrating higher consumption of human milk oligosaccharides by B. infantis EVC001. Concentrations of acetate and lactate were significantly higher and fecal pH was significantly lower in infants fed EVC001, demonstrating alterations in intestinal fermentation. Infants colonized by Bifidobacteriaceae at high levels had 4-fold-lower fecal endotoxin levels, consistent with observed lower levels of Gram-negative Proteobacteria and Bacteroidetes. IMPORTANCE The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function.

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