scholarly journals Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria

2021 ◽  
Author(s):  
Nicholas A Pudlo ◽  
Karthik Urs ◽  
Ryan Crawford ◽  
Ali Pirani ◽  
Todd Atherly ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Human Colon ◽  
Symbiotic Bacteria ◽  
Complex Carbohydrate ◽  
Human Gut ◽  
Carbohydrate Utilization ◽  
Bacteroides Ovatus ◽  
The Relationship ◽  
Carbohydrate Digestion ◽  
Insight Into

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.

scholarly journals Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Yunus E. Tuncil ◽  
Yao Xiao ◽  
Nathan T. Porter ◽  
Bradley L. Reuhs ◽  
Eric C. Martens ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Human Colon ◽  
Competitive Environment ◽  
Energy Requirements ◽  
Human Gut ◽  
Carbohydrate Utilization ◽  
Stable Coexistence ◽  
Complex Carbohydrates ◽  
Improve Health

ABSTRACT When presented with nutrient mixtures, several human gut Bacteroides species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression. However, it is unclear how closely these observed physiological changes, often measured by altered transcription of glycan utilization genes, mirror actual glycan depletion. To understand the glycan prioritization strategies of two closely related human gut symbionts, Bacteroides ovatus and Bacteroides thetaiotaomicron, we performed a series of time course assays in which both species were individually grown in a medium with six different glycans that both species can degrade. Disappearance of the substrates and transcription of the corresponding polysaccharide utilization loci (PULs) were measured. Each species utilized some glycans before others, but with different priorities per species, providing insight into species-specific hierarchical preferences. In general, the presence of highly prioritized glycans repressed transcription of genes involved in utilizing lower-priority nutrients. However, transcriptional sensitivity to some glycans varied relative to the residual concentration in the medium, with some PULs that target high-priority substrates remaining highly expressed even after their target glycan had been mostly depleted. Coculturing of these organisms in the same mixture showed that the hierarchical orders generally remained the same, promoting stable coexistence. Polymer length was found to be a contributing factor for glycan utilization, thereby affecting its place in the hierarchy. Our findings not only elucidate how B. ovatus and B. thetaiotaomicron strategically access glycans to maintain coexistence but also support the prioritization of carbohydrate utilization based on carbohydrate structure, advancing our understanding of the relationships between diet and the gut microbiome. IMPORTANCE The microorganisms that reside in the human colon fulfill their energy requirements mainly from diet- and host-derived complex carbohydrates. Members of this ecosystem possess poorly understood strategies to prioritize and compete for these nutrients. Based on direct carbohydrate measurements and corresponding transcriptional analyses, our findings showed that individual bacterial species exhibit different preferences for the same set of glycans and that this prioritization is maintained in a competitive environment, which may promote stable coexistence. Such understanding of gut bacterial glycan utilization will be essential to eliciting predictable changes in the gut microbiota to improve health through the diet. IMPORTANCE The microorganisms that reside in the human colon fulfill their energy requirements mainly from diet- and host-derived complex carbohydrates. Members of this ecosystem possess poorly understood strategies to prioritize and compete for these nutrients. Based on direct carbohydrate measurements and corresponding transcriptional analyses, our findings showed that individual bacterial species exhibit different preferences for the same set of glycans and that this prioritization is maintained in a competitive environment, which may promote stable coexistence. Such understanding of gut bacterial glycan utilization will be essential to eliciting predictable changes in the gut microbiota to improve health through the diet.

scholarly journals A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle

2019 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Jarmo Ritari ◽  
Lars Paulin ◽  
Ger T. Rijkers ◽  
...  
Keyword(s):  
Anaerobic Respiration ◽  
Gene Clusters ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Carbohydrate Utilization ◽  
Soil Isolate ◽  
The Family ◽  
Intestinal Origin ◽  
The Common ◽  
Insight Into

AbstractCultivation-independent surveys have shown that the recently described genus Romboutsia within the family Peptostreptococcaceae is more diverse than previously acknowledged. The majority of Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles that Romboutsia species play in the digestive tract are largely unknown. The complete genomes of the human intestinal isolate Romboutsia hominis FRIFIT (DSM 28814) and the soil isolate Romboutsia lituseburensis A25KT (DSM 797) were sequenced. An evaluation of the common traits of this recently defined genus was done based on comparative genome analysis of the two strains together with the previously elucidated genome of the type species Romboutsia ilealis CRIBT. These analyses showed that the genus Romboutsia covers a broad range of metabolic capabilities with respect to carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end products. Main differences between strains were found in their abilities to utilize specific carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. In addition, differences were found with respect to bile metabolism and motility-related gene clusters.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

On Metaphysics and the Political: A Polemics of Reading Baudelaire in the 1930s

2019 ◽  
Vol 58 (2) ◽  
pp. 249-259
Author(s):  
Joseph Acquisto
Keyword(s):  
Twentieth Century ◽  
Political Crisis ◽  
The Political ◽  
Modern Poetry ◽  
Progressive Politics ◽  
The World ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

This essay examines a polemic between two Baudelaire critics of the 1930s, Jean Cassou and Benjamin Fondane, which centered on the relationship of poetry to progressive politics and metaphysics. I argue that a return to Baudelaire's poetry can yield insight into what seems like an impasse in Cassou and Fondane. Baudelaire provides the possibility of realigning metaphysics and politics so that poetry has the potential to become the space in which we can begin to think the two of them together, as opposed to seeing them in unresolvable tension. Or rather, the tension that Baudelaire animates between the two allows us a new way of thinking about the role of esthetics in moments of political crisis. We can in some ways see Baudelaire as responding, avant la lettre, to two of his early twentieth-century readers who correctly perceived his work as the space that breathes a new urgency into the questions of how modern poetry relates to the world from which it springs and in which it intervenes.

The Annual Reports of the Prison Commissioners for Scotland and Religion, 1903–1931

2019 ◽  
Vol 48 (1) ◽  
pp. 83-101
Author(s):  
Cameron McKay
Keyword(s):  
Annual Report ◽  
Annual Reports ◽  
Individual Choice ◽  
Drinking Habits ◽  
Parental Neglect ◽  
Late Nineteenth ◽  
Causes Of Crime ◽  
Criminological Theories ◽  
The Relationship ◽  
Insight Into

During the late nineteenth and early twentieth century penologists began to explore the possibility that environment and upbringing, as opposed to individual choice, were the causes criminality. The Prison Commissioners for Scotland, the devolved body who administered prisons north of the border, were not immune to this wider trend. Smith has argued that from the 1890s onwards the Commissioners began to accept that criminality was caused by social problems, namely alcoholism, but also parental neglect, poor education and poverty. In their efforts to test these new criminological theories, the Commissioners began to make more careful enquiries into the backgrounds of their charges. From 1896 to 1931 the Commissioners interviewed a sample of prisoners each year and included the findings in their annual report. Although the main focus of these interviews was on the upbringing and drinking habits of prisoners; by the 1900s the Commissioners seem to have added irreligion to the growing list of etiological causes of crime, and from 1903 onwards prisoners were asked to give details on their religious habits. Although it is debateable how much the Prison Commissioners revealed about the relationship between religion and crime, they did however provide a useful insight into the religiosity of the average prisoner.

The Relationship between Seeker and Spiritual Guide as portrayed in contemporary Western Sufi Autobiographies

2011 ◽  
Vol 5 (2) ◽  
pp. 297-332
Author(s):  
Kate Zebiri
Keyword(s):  
Life Writing ◽  
New Age ◽  
The Self ◽  
Individual Autonomy ◽  
Religious Authority ◽  
The Face ◽  
The Relationship ◽  
Insight Into ◽  
Continuity And Discontinuity

This article aims to explore the Shaykh-mur?d (disciple) or teacher-pupil relationship as portrayed in Western Sufi life writing in recent decades, observing elements of continuity and discontinuity with classical Sufism. Additionally, it traces the influence on the texts of certain developments in religiosity in contemporary Western societies, especially New Age understandings of religious authority. Studying these works will provide an insight into the diversity of expressions of contemporary Sufism, while shedding light on a phenomenon which seems to fly in the face of contemporary social and religious trends which deemphasize external authority and promote the authority of the self or individual autonomy.

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon

2020 ◽  
Author(s):  
CC Kim ◽  
GR Healey ◽  
WJ Kelly ◽  
ML Patchett ◽  
Z Jordens ◽  
...  
Keyword(s):  
Cell Surface ◽  
Degradation Products ◽  
Model Organism ◽  
Human Colon ◽  
Surface Proteins ◽  
Human Gut ◽  
Pectate Lyases ◽  
Unusual Distribution ◽  
Degrading Bacteria ◽  
Acetyl Esterases

© 2019, International Society for Microbial Ecology. Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

Empathy as moderator of gender differences in Chinese insurance agents' business ethical sensitivity

2017 ◽  
Vol 45 (6) ◽  
pp. 1029-1042 ◽  
Author(s):  
Na Zhang ◽  
Jian Zhang ◽  
Jing Wang
Keyword(s):  
Gender Differences ◽  
Business Ethics ◽  
Research Field ◽  
Ethical Sensitivity ◽  
Men And Women ◽  
Insurance Agents ◽  
Factors Associated ◽  
Ethics Research ◽  
The Relationship ◽  
Insight Into

To expand the business ethics research field, and to increase society's understanding of Chinese insurance agents' business ethics, we investigated how gender differences are related to agents' business ethical sensitivity and whether or not these relationships are moderated by empathy. Through a regression analysis of the factors associated with the business ethical sensitivity of 417 Chinese insurance agents, we found that gender played an important role in affecting business ethical sensitivity, and empathy significantly affected business ethical sensitivity. Furthermore, empathy had a moderating effect on the relationship between gender and business ethical sensitivity. Both men and women with strong empathy scored high on business ethical sensitivity; however, men with strong empathy had higher levels of business ethical sensitivity than did women with little empathy. The findings add to the literature by providing insight into the mechanisms responsible for the benefits of empathy in increasing business ethical sensitivity.

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