scholarly journals Genome Reduction inPsychromonasSpecies within the Gut of an Amphipod from the Ocean’s Deepest Point

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Weipeng Zhang ◽  
Ren-Mao Tian ◽  
Jin Sun ◽  
Salim Bougouffa ◽  
Wei Ding ◽  
...  
Keyword(s):  
Nutrient Utilization ◽  
Microbial Composition ◽  
Free Living ◽  
Carbohydrate Utilization ◽  
Mariana Trench ◽  
Associated Bacteria ◽  
Content Type ◽  
Genomic Analyses ◽  
And Function ◽  
Central Carbohydrate Metabolism

ABSTRACTAmphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth’s oceans. Here the gut microbiota of the amphipodHirondellea gigascollected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated byPsychromonas, of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-livingPsychromonasstrains, CDP1 has a highly reduced genome. Genome alignment showed deletion of the trimethylamineN-oxide (TMAO) reducing gene cluster in CDP1, suggesting that the “piezolyte” function of TMAO is more important than its function in respiration, which may lead to TMAO accumulation. In terms of nutrient utilization, the bacterium retains its central carbohydrate metabolism but lacks most of the extended carbohydrate utilization pathways, suggesting the confinement ofPsychromonasto the host gut and sequestration from more variable environmental conditions. Moreover, CDP1 contains a complete formate hydrogenlyase complex, which might be involved in energy production. The genomic analyses imply that CDP1 may have developed adaptive strategies for a lifestyle within the gut of the hadal amphipodH. gigas.IMPORTANCEAs a unique but poorly investigated habitat within marine ecosystems, hadal trenches have received interest in recent years. This study explores the gut microbial composition and function in hadal amphipods, which are among the dominant carrion feeders in hadal habitats. Further analyses of a dominant strain revealed genomic features that may contribute to its adaptation to the amphipod gut environment. Our findings provide new insights into animal-associated bacteria in the hadal biosphere.

scholarly journals 370 Awardee Talk: Role of feed enzymes in gut health and function

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 111-112
Author(s):  
Charles Martin Nyachoti
Keyword(s):  
Pathogenic Bacteria ◽  
Production Systems ◽  
Nutrient Utilization ◽  
Gut Health ◽  
Microbial Composition ◽  
Medication Costs ◽  
Feed Enzymes ◽  
Enzyme Supplementation ◽  
And Function

Abstract Exogenous enzymes are routinely added to diets for non-ruminant animals, mainly to help enhance energy and nutrient utilization, thus contributing to efficient and sustainable production systems. Also, feed enzymes allow for effective utilization of non-traditional feedstuffs (e.g. co-products) in non-ruminant diets, with potential to mitigate feed cost. In addition to increased nutrient utilization, however, feed enzymes, through their impact on the gastrointestinal environment and microbial composition, can have a profound effect on indices of gut health and function. These effects may explain the reported reductions in medication costs and variability in animal performance and mortality rates observed with dietary enzyme supplementation. By acting on their target substrates, feed enzymes reduce the availability of non-digested substrates and in the case of carbohydrate-degrading enzymes can produce short-chain oligosaccharides with potential prebiotic effects. These changes are known to modulate the gut microbiome in favor of bacteria associated with a healthy gut, while reducing the population of pathogenic bacteria, which explains the reduced incidences of diarrhea that have been attributed to enzyme supplementation. Also, feed enzymes may reduce oxidative stress and enhance the functional capacity (e.g. maintaining barrier function) of the gastrointestinal tract. Feed enzymes by themselves may never be a single solution to mitigate gut health challenges in livestock production systems, but clearly there is a mounting body of evidence to support the role of feed enzymes in this regard. Therefore, their benefits will be maximized when used as part of an integrated solution approach for containing enteric pathogens of economic importance and eliminating the negative effects of dietary components with potential to compromise intestinal integrity.

scholarly journals Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan

2015 ◽  
Vol 197 (9) ◽  
pp. 1538-1548 ◽  
Author(s):  
Varsha Raghavan ◽  
Eduardo A. Groisman
Keyword(s):  
Chondroitin Sulfate ◽  
Related Species ◽  
Bacterial Species ◽  
Nutrient Utilization ◽  
Gut Bacteria ◽  
Dynamic Responses ◽  
Microbial Composition ◽  
Specific Expression ◽  
Content Type ◽  
Species Specific

ABSTRACTThe mammalian intestine provides nutrients to hundreds of bacterial species. Closely related species often harbor homologous nutrient utilization genes and cocolonize the gut, raising questions regarding the strategies mediating their stable coexistence. Here we reveal that relatedBacteroidesspecies that can utilize the mammalian glycan chondroitin sulfate (CS) have diverged in the manner in which they temporally regulate orthologous CS utilization genes. Whereas certainBacteroidesspecies display a transient surge in CS utilization transcripts upon exposure to CS, other species exhibit sustained activation of these genes. Remarkably, species-specific expression dynamics are retained even when the key players governing a particular response are replaced by those from a species with a dissimilar response.Bacteroidesspecies exhibiting distinct expression behaviors in the presence of CS can be cocultured on CS. However, they vary in their responses to CS availability and to the composition of the bacterial community when CS is the sole carbon source. Our results indicate that diversity resulting from regulation of polysaccharide utilization genes may enable the coexistence of gut bacterial species using a given nutrient.IMPORTANCEGenes mediating a specific task are typically conserved in related microbes. For instance, gutBacteroidesspecies harbor orthologous nutrient breakdown genes and may face competition from one another for these nutrients. How, then, does the gut microbial composition maintain such remarkable stability over long durations? We establish that in the case of genes conferring the ability to utilize the nutrient chondroitin sulfate (CS), microbial species vary in how they temporally regulate these genes and exhibit subtle growth differences on the basis of CS availability and community composition. Similarly to how differential regulation of orthologous genes enables related species to access new environments, gut bacteria may regulate the same genes in distinct fashions to reduce the overlap with coexisting species for utilization of available nutrients.

scholarly journals Ecology and Biotechnological Potential of Bacteria Belonging to the GenusPseudovibrio

2018 ◽  
Vol 84 (8) ◽  
Author(s):  
Stefano Romano
Keyword(s):  
Marine Invertebrates ◽  
Marine Sponges ◽  
Nutrient Cycles ◽  
Free Living ◽  
Associated Bacteria ◽  
Biotechnological Potential ◽  
Content Type ◽  
Tropical Regions ◽  
Marine Systems ◽  
Major Nutrient

ABSTRACTMembers of the genusPseudovibriohave been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally,Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities ofPseudovibriospp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.

scholarly journals Gut Microbial Divergence between Two Populations of the Hadal AmphipodHirondellea gigas

2018 ◽  
Vol 85 (1) ◽  
Author(s):  
Weipeng Zhang ◽  
Hiromi Kayama Watanabe ◽  
Wei Ding ◽  
Yi Lan ◽  
Ren-Mao Tian ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Taxonomic Composition ◽  
Microbial Interactions ◽  
Japan Trench ◽  
Microbial Composition ◽  
Mariana Trench ◽  
Content Type ◽  
Alpha And Beta Diversity ◽  
Functional Potential

ABSTRACTHadal environments sustain diverse microorganisms. A few studies have investigated hadal microbial communities consisting of free-living or particle-associated bacteria and archaea. However, animal-associated microbial communities in hadal environments remain largely unexplored, and comparative analyses of animal gut microbiota between two isolated hadal environments have never been done so far. In the present study, 228 Gb of gut metagenomes of the giant amphipodHirondellea gigasfrom two hadal trenches, the Mariana Trench and Japan Trench, were sequenced and analyzed. Taxonomic analysis identified 49 microbial genera commonly shared by the gut microbiota of the twoH. gigaspopulations. However, the results of statistical analysis, in congruency with the alpha and beta diversity analyses, revealed significant differences in gut microbial composition across the two trenches. Abundance variation ofPsychromonas,Propionibacterium, andPseudoalteromonasspecies was observed. Microbial cooccurrence was demonstrated for microbes that were overrepresented in the Mariana trench. Comparison of functional potential showed that the percentage of carbohydrate metabolic genes among the total microbial genes was significantly higher in the guts ofH. gigasspecimens from the Mariana Trench. Integrating carbon input information and geological characters of the two hadal trenches, we propose that the differences in the community structure might be due to several selective factors, such as environmental variations and microbial interactions.IMPORTANCEThe taxonomic composition and functional potential of animal gut microbiota in deep-sea environments remain largely unknown. Here, by performing comparative metagenomics, we suggest that the gut microbial compositions of twoHirondellea gigaspopulations from the Mariana Trench and the Japan Trench have undergone significant divergence. Through analyses of functional potentials and microbe-microbe correlations, our findings shed light on the contributions of animal gut microbiota to host adaptation to hadal environments.

scholarly journals A Five-Ingredient Nutritional Supplement and Home-Based Resistance Exercise Improve Lean Mass and Strength in Free-Living Elderly

Nutrients ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2391 ◽  
Author(s):  
Mats I. Nilsson ◽  
Andrew Mikhail ◽  
Lucy Lan ◽  
Alessia Di Carlo ◽  
Bethanie Hamilton ◽  
...  
Keyword(s):  
Resistance Exercise ◽  
Old Age ◽  
Body Fat ◽  
Lean Mass ◽  
Daily Intake ◽  
Protein Supplementation ◽  
Muscle Quality ◽  
Free Living ◽  
Home Based ◽  
And Function

Old age is associated with lower physical activity levels, suboptimal protein intake, and desensitization to anabolic stimuli, predisposing for age-related muscle loss (sarcopenia). Although resistance exercise (RE) and protein supplementation partially protect against sarcopenia under controlled conditions, the efficacy of home-based, unsupervised RE (HBRE) and multi-ingredient supplementation (MIS) is largely unknown. In this randomized, placebo-controlled and double-blind trial, we examined the effects of HBRE/MIS on muscle mass, strength, and function in free-living, older men. Thirty-two sedentary men underwent twelve weeks of home-based resistance band training (3 d/week), in combination with daily intake of a novel five-nutrient supplement (‘Muscle5’; M5, n = 16, 77.4 ± 2.8 y) containing whey, micellar casein, creatine, vitamin D, and omega-3 fatty acids, or an isocaloric/isonitrogenous placebo (PLA; n = 16, 74.4 ± 1.3 y), containing collagen and sunflower oil. Appendicular and total lean mass (ASM; +3%, TLM; +2%), lean mass to fat ratios (ASM/% body fat; +6%, TLM/% body fat; +5%), maximal strength (grip; +8%, leg press; +17%), and function (5-Times Sit-to-Stand time; −9%) were significantly improved in the M5 group following HBRE/MIS therapy (pre vs. post tests; p < 0.05). Fast-twitch muscle fiber cross-sectional areas of the quadriceps muscle were also significantly increased in the M5 group post intervention (Type IIa; +30.9%, Type IIx, +28.5%, p < 0.05). Sub-group analysis indicated even greater gains in total lean mass in sarcopenic individuals following HBRE/MIS therapy (TLM; +1.65 kg/+3.4%, p < 0.05). We conclude that the Muscle5 supplement is a safe, well-tolerated, and effective complement to low-intensity, home-based resistance exercise and improves lean mass, strength, and overall muscle quality in old age.

scholarly journals Exploring the microbiome in health and disease

2017 ◽  
Vol 1 ◽  
pp. 239784731774188 ◽  
Author(s):  
Elena Scotti ◽  
Stéphanie Boué ◽  
Giuseppe Lo Sasso ◽  
Filippo Zanetti ◽  
Vincenzo Belcastro ◽  
...  
Keyword(s):  
Human Health ◽  
Metabolic Diseases ◽  
Skin Diseases ◽  
Human Microbiome ◽  
Chronic Obstructive ◽  
Microbial Composition ◽  
Obstructive Pulmonary Disease ◽  
New Findings ◽  
Dynamics And Function ◽  
And Function

The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.

scholarly journals Stoichiometry and Turnover of the Bacterial Flagellar Switch Protein FliN

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Nicolas J. Delalez ◽  
Richard M. Berry ◽  
Judith P. Armitage
Keyword(s):  
Copy Number ◽  
Motor Proteins ◽  
Fluorescent Protein ◽  
Protein Complexes ◽  
Content Type ◽  
Rotation Direction ◽  
Cell Measurement ◽  
Biological Complexes ◽  
And Function

ABSTRACTSome proteins in biological complexes exchange with pools of free proteins while the complex is functioning. Evidence is emerging that protein exchange can be part of an adaptive mechanism. The bacterial flagellar motor is one of the most complex biological machines and is an ideal model system to study protein dynamics in large multimeric complexes. Recent studies showed that the copy number of FliM in the switch complex and the fraction of FliM that exchanges vary with the direction of flagellar rotation. Here, we investigated the stoichiometry and turnover of another switch complex component, FliN, labeled with the fluorescent protein CyPet, inEscherichia coli. Our results confirm that,in vivo, FliM and FliN form a complex with stoichiometry of 1:4 and function as a unit. We estimated that wild-type motors contained 120 ± 26 FliN molecules. Motors that rotated only clockwise (CW) or counterclockwise (CCW) contained 114 ± 17 and 144 ± 26 FliN molecules, respectively. The ratio of CCW-to-CW FliN copy numbers was 1.26, very close to that of 1.29 reported previously for FliM. We also measured the exchange of FliN molecules, which had a time scale and dependence upon rotation direction similar to those of FliM, consistent with an exchange of FliM-FliN as a unit. Our work confirms the highly dynamic nature of multimeric protein complexes and indicates that, under physiological conditions, these machines might not be the stable, complete structures suggested by averaged fixed methodologies but, rather, incomplete rings that can respond and adapt to changing environments.IMPORTANCEThe flagellum is one of the most complex structures in a bacterial cell, with the core motor proteins conserved across species. Evidence is now emerging that turnover of some of these motor proteins depends on motor activity, suggesting that turnover is important for function. The switch complex transmits the chemosensory signal to the rotor, and we show, by using single-cell measurement, that both the copy number and the fraction of exchanging molecules vary with the rotational bias of the rotor. When the motor is locked in counterclockwise rotation, the copy number is similar to that determined by averaged, fixed methodologies, but when locked in a clockwise direction, the number is much lower, suggesting that that the switch complex ring is incomplete. Our results suggest that motor remodeling is an important component in tuning responses and adaptation at the motor.

Neurodevelopment in the first three years: implications for child development, professional practice and policy

2014 ◽  
Vol 9 (2) ◽  
pp. 154-164 ◽  
Author(s):  
Danya Glaser
Keyword(s):  
Brain Development ◽  
Brain Activity ◽  
Brain Maturation ◽  
Policy And Practice ◽  
Content Type ◽  
Key Issues ◽  
And Function ◽  
The Relationship ◽  
The Brain ◽  
Brain Connections

Purpose – The purpose of this paper is to outline brain structure and development, the relationship between environment and brain development and implications for practice. Design/methodology/approach – The paper is based on a selected review of the literature and clinical experience. Findings – While genetics determine the sequence of brain maturation, the nature of brain development and functioning is determined by the young child's caregiving environment, to which the developing brain constantly adapts. The absence of input during sensitive periods may lead to later reduced functioning. There is an undoubted immediate equivalence between every mind function – emotion, cognition, behaviour and brain activity, although the precise location of this in the brain is only very partially determinable, since brain connections and function are extremely complex. Originality/value – This paper provides an overview of key issues in neurodevelopment relating to the development of young children, and implications for policy and practice.

scholarly journals Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park

2015 ◽  
Vol 81 (17) ◽  
pp. 5907-5916 ◽  
Author(s):  
Z. J. Jay ◽  
J. P. Beam ◽  
A. Dohnalkova ◽  
R. Lohmayer ◽  
B. Bodle ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Elemental Sulfur ◽  
De Novo ◽  
Hot Spring ◽  
Content Type ◽  
Physiological Attributes ◽  
And Function ◽  
Metagenome Sequence

ABSTRACTThermoproteales(phylumCrenarchaeota) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolatePyrobaculum yellowstonensisstrain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurringin situ. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for thede novosynthesis of nearly all required cofactors and metabolites were identified. The comparative genomics ofP. yellowstonensisand the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) toin situpopulations. The physiological attributes and metabolic capabilities ofP. yellowstonensisprovide an important foundation for developing an understanding of the distribution and function of these populations in YNP.

Reflections on team culture, structure and function of an intensive support service centred on positive behavioural support

2016 ◽  
Vol 21 (4) ◽  
pp. 203-211 ◽  
Author(s):  
Lawrence A. Patterson ◽  
Samuel Berry
Keyword(s):  
Social Services ◽  
Support Service ◽  
Structure And Function ◽  
Content Type ◽  
Case Examples ◽  
Behavioural Support ◽  
Team Culture ◽  
Shared Identity ◽  
The Right ◽  
And Function

Purpose The purpose of this paper is to explore experiences of team culture, structure and function of an intensive support service (ISS) within the context of the recent service guidance “Building the Right Support” (NHS England, Local Government Association and Association of Directors of Adult Social Services, 2015). Reflections on the Hampshire and Southampton ISS set up in 2010 are discussed with a view to informing a debate about frameworks for ISS services nationally. Design/methodology/approach A reflective piece, drawing on experience and case examples. Findings This paper describes that a key function of an ISS is making individuals safe and this is significantly assisted by using shared team formulation, which can enable information and perspectives to be shared between and within teams as rapidly as possible. Further, a case is made for recognising the importance of inter-disciplinary practice, as the Southampton and Hampshire ISS has removed the “old fashioned” demarcations that led to individuals seeing a “procession” of different professionals from different disciplines. This relates to team structure, but importantly is about a culture of holding a shared identity based on positive behavioural support values, rather than a traditional uni-disciplinary perspective. Practical implications ISS models are being proposed by NHS England and this paper suggests some important practical aspects. Originality/value Limited literature exists examining the team culture within ISSs, which contributes to desired outcomes for service users. This paper opens a debate about structural and functional aspects of service delivery in this service model.

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