scholarly journals Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus

2020 ◽  
Author(s):  
Xingkun Jin ◽  
Ziwei Chen ◽  
Yan Shi ◽  
Jian-Fang Gui ◽  
Zhe Zhao
Keyword(s):  
Growth Rate ◽  
Gut Microbiota ◽  
Slow Growth ◽  
Ecological Processes ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Environmental Bacteria ◽  
Feed Source ◽  
Host Microbe Interactions ◽  
Insight Into

ABSTRACTUnderstanding the ecological processes in controlling the assemblage of gut microbiota becomes an essential prerequisite for a more sustainable aquaculture. Here we used 16S rRNA amplicon sequencing to characterize the hindgut microbiota from cultured obscure puffer Takifugu obscurus. The gut microbiota is featured with lower alpha-diversity, greater beta-dispersion and higher average 16S rRNA copy numbers comparing to water and sediment, but far less so to feed. SourceTracker predicted a notable source signature from feed in gut microbiota. Furthermore, effect of varying degrees of feed-associated bacteria on compositional, functional and phylogenetic diversity of gut microbiota were revealed. Coincidently, considerable increase of species richness and feed source proportions both were observed in slow growth fugu, implying a reduced stability in gut microbiota upon bacterial disturbance from feed. Moreover, quantitative ecological analytic framework was applied and the ecological processes underlying such community shift were determined. In the context of lower degree of feed disturbance, homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts. Whilst with the degree of feed disturbance increased, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Altogether, our findings illustrated a clear diversity-function relationships in fugu gut microbiota, and it has implicated in a strong correlation between feed-borne bacteria and host growth rate. These results provide a new insight into aquaculture of fugu and other economically important fishes, as well as a better understanding of host-microbe interactions in the vertebrate gastrointestinal tract.IMPORTANCEEnvironmental bacteria has a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon fugu gut microbiota. As a result, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, which is potentially correlated with the host physiological condition such as gastric evacuation rate. Our findings emphasized the intricate linkage between feed and gut microbiota, and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes, and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.

scholarly journals Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Ryan S. Nett ◽  
Huy Nguyen ◽  
Raimund Nagel ◽  
Ariana Marcassa ◽  
Trevor C. Charles ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genetic Heterogeneity ◽  
Evolutionary History ◽  
Biosynthetic Gene Cluster ◽  
Evolutionary Analysis ◽  
Biosynthetic Gene ◽  
Ancestral Gene ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Insight Into

ABSTRACT Gibberellin (GA) phytohormones are ubiquitous regulators of growth and developmental processes in vascular plants. The convergent evolution of GA production by plant-associated bacteria, including both symbiotic nitrogen-fixing rhizobia and phytopathogens, suggests that manipulation of GA signaling is a powerful mechanism for microbes to gain an advantage in these interactions. Although orthologous operons encode GA biosynthetic enzymes in both rhizobia and phytopathogens, notable genetic heterogeneity and scattered operon distribution in these lineages, including loss of the gene for the final biosynthetic step in most rhizobia, suggest varied functions for GA in these distinct plant-microbe interactions. Therefore, deciphering GA operon evolutionary history should provide crucial evidence toward understanding the distinct biological roles for bacterial GA production. To further establish the genetic composition of the GA operon, two operon-associated genes that exhibit limited distribution among rhizobia were biochemically characterized, verifying their roles in GA biosynthesis. This enabled employment of a maximum parsimony ancestral gene block reconstruction algorithm to characterize loss, gain, and horizontal gene transfer (HGT) of GA operon genes within alphaproteobacterial rhizobia, which exhibit the most heterogeneity among the bacteria containing this biosynthetic gene cluster. Collectively, this evolutionary analysis reveals a complex history for HGT of the entire GA operon, as well as the individual genes therein, and ultimately provides a basis for linking genetic content to bacterial GA functions in diverse plant-microbe interactions, including insight into the subtleties of the coevolving molecular interactions between rhizobia and their leguminous host plants. IMPORTANCE While production of phytohormones by plant-associated microbes has long been appreciated, identification of the gibberellin (GA) biosynthetic operon in plant-associated bacteria has revealed surprising genetic heterogeneity. Notably, this heterogeneity seems to be associated with the lifestyle of the microbe; while the GA operon in phytopathogenic bacteria does not seem to vary to any significant degree, thus enabling production of bioactive GA, symbiotic rhizobia exhibit a number of GA operon gene loss and gain events. This suggests that a unique set of selective pressures are exerted on this biosynthetic gene cluster in rhizobia. Through analysis of the evolutionary history of the GA operon in alphaproteobacterial rhizobia, which display substantial diversity in their GA operon structure and gene content, we provide insight into the effect of lifestyle and host interactions on the production of this phytohormone by plant-associated bacteria.

scholarly journals Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Ragnhild I Vestrum ◽  
Kari J K Attramadal ◽  
Olav Vadstein ◽  
Madeleine Stenshorne Gundersen ◽  
Ingrid Bakke
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Atlantic Cod ◽  
Animal Health ◽  
Striking Difference ◽  
Ecological Processes ◽  
Opportunistic Bacteria ◽  
Atlantic Cod Larvae ◽  
Microbe Interactions ◽  
Host Microbe Interactions

ABSTRACT Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host–microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host–microbe interactions and improved fish health and survival.

Host-microbe interactions mediating antitumorigenic effects of MRX0518, a gut microbiota-derived bacterial strain, in breast, renal and lung carcinoma.

2018 ◽  
Vol 36 (15_suppl) ◽  
pp. e15006-e15006 ◽  
Author(s):  
Alex Stevenson ◽  
Alessio Panzica ◽  
Amy Holt ◽  
Delphine Laute Caly ◽  
Anna Ettore ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Lung Carcinoma ◽  
Bacterial Strain ◽  
Microbe Interactions ◽  
Host Microbe Interactions

scholarly journals Structural basis of ligand selectivity by a bacterial adhesin lectin involved in multi- species biofilm formation

2020 ◽  
Author(s):  
Shuaiqi Guo ◽  
Tyler D.R. Vance ◽  
Hossein Zahiri ◽  
Robert Eves ◽  
Corey Stevens ◽  
...  
Keyword(s):  
High Resolution ◽  
Biofilm Formation ◽  
Molecular Basis ◽  
Symbiotic Bacterium ◽  
Structural Basis ◽  
Ligand Selectivity ◽  
End Groups ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Insight Into

AbstractCarbohydrate recognition by lectins governs critical host-microbe interactions. MpPA14 lectin is a domain of a 1.5-MDa adhesin responsible for a symbiotic bacterium-diatom interaction in Antarctica. Here we show MpPA14 binds various monosaccharides, with L-fucose and N-acetyl glucosamine being the strongest ligands (Kd ~ 150 μM). High-resolution structures of MpPA14 with 15 different sugars bound elucidated the molecular basis for the lectin’s apparent binding promiscuity but underlying selectivity. MpPA14 mediates strong Ca2+-dependent interactions with the 3, 4 diols of L-fucopyranose and glucopyranoses, and binds other sugars via their specific minor isomers. Thus, MpPA14 only binds polysaccharides like branched glucans and fucoidans with these free end-groups. Consistent with our findings, adhesion of MpPA14 to diatom cells was selectively blocked by L-fucose, but not by N-acetyl galactosamine. With MpPA14 lectin homologs present in adhesins of several pathogens, our work gives insight into an anti-adhesion strategy to block infection via ligand-based antagonists.

scholarly journals Conserved bases for the initial cyclase in gibberellin biosynthesis: from bacteria to plants

2019 ◽  
Vol 476 (18) ◽  
pp. 2607-2621 ◽  
Author(s):  
Cody Lemke ◽  
Kevin C. Potter ◽  
Samuel Schulte ◽  
Reuben J. Peters
Keyword(s):  
Catalytic Mechanism ◽  
Phylogenetic Analyses ◽  
Gibberellin Biosynthesis ◽  
Associated Bacteria ◽  
Functional Conservation ◽  
Microbe Interactions ◽  
Bacteria And Fungi ◽  
Product Outcome ◽  
Insight Into ◽  
Ga Biosynthesis

Abstract All land plants contain at least one class II diterpene cyclase (DTC), which utilize an acid-base catalytic mechanism, for the requisite production of ent-copalyl diphosphate (ent-CPP) in gibberellin A (GA) phytohormone biosynthesis. These ent-CPP synthases (CPSs) are hypothesized to be derived from ancient bacterial origins and, in turn, to have given rise to the frequently observed additional DTCs utilized in more specialized plant metabolism. However, such gene duplication and neo-functionalization has occurred repeatedly, reducing the utility of phylogenetic analyses. Support for evolutionary scenarios can be found in more specific conservation of key enzymatic features. While DTCs generally utilize a DxDD motif as the catalytic acid, the identity of the catalytic base seems to vary depending, at least in part, on product outcome. The CPS from Arabidopsis thaliana has been found to utilize a histidine-asparagine dyad to ligate a water molecule that serves as the catalytic base, with alanine substitution leading to the production of 8β-hydroxy-ent-CPP. Here this dyad and effect of Ala substitution is shown to be specifically conserved in plant CPSs involved in GA biosynthesis, providing insight into plant DTC evolution and assisting functional assignment. Even more strikingly, while GA biosynthesis arose independently in plant-associated bacteria and fungi, the catalytic base dyad also is specifically found in the relevant bacterial, but not fungal, CPSs. This suggests functional conservation of CPSs from bacteria to plants, presumably reflecting an early role for derived diterpenoids in both plant development and plant–microbe interactions, eventually leading to GA, and a speculative evolutionary scenario is presented.

scholarly journals Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners

2019 ◽  
Vol 11 (3) ◽  
pp. 616-629 ◽  
Author(s):  
Sara C Di Rienzi ◽  
Robert A Britton
Keyword(s):  
Gut Microbiota ◽  
Intestinal Tract ◽  
Western Diet ◽  
Health Concerns ◽  
Diet Cost ◽  
Microbe Interactions ◽  
Novel Approaches ◽  
Host Microbe Interactions ◽  
Genetic Profiles ◽  
Dietary Sugars

ABSTRACT The consumption of sugar has become central to the Western diet. Cost and health concerns associated with sucrose spurred the development and consumption of other sugars and sweeteners, with the average American consuming 10 times more sugar than 100 y ago. In this review, we discuss how gut microbes are affected by changes in the consumption of sugars and other sweeteners through transcriptional, abundance, and genetic adaptations. We propose that these adaptations result in microbes taking on different metabolic, ecological, and genetic profiles along the intestinal tract. We suggest novel approaches to assess the consequences of these changes on host–microbe interactions to determine the safety of novel sugars and sweeteners.

scholarly journals Gut Microbial Influences on the Mammalian Intestinal Stem Cell Niche

2017 ◽  
Vol 2017 ◽  
pp. 1-17 ◽  
Author(s):  
Bailey C. E. Peck ◽  
Michael T. Shanahan ◽  
Ajeet P. Singh ◽  
Praveen Sethupathy
Keyword(s):  
Stem Cell ◽  
Gut Microbiota ◽  
Energy Homeostasis ◽  
Environmental Changes ◽  
Intestinal Epithelial ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Cell Niche ◽  
Systemic Health ◽  
Endocrine Signaling

The mammalian intestinal epithelial stem cell (IESC) niche is comprised of diverse epithelial, immune, and stromal cells, which together respond to environmental changes within the lumen and exert coordinated regulation of IESC behavior. There is growing appreciation for the role of the gut microbiota in modulating intestinal proliferation and differentiation, as well as other aspects of intestinal physiology. In this review, we evaluate the diverse roles of known niche cells in responding to gut microbiota and supporting IESCs. Furthermore, we discuss the potential mechanisms by which microbiota may exert their influence on niche cells and possibly on IESCs directly. Finally, we present an overview of the benefits and limitations of available tools to study niche-microbe interactions and provide our recommendations regarding their use and standardization. The study of host-microbe interactions in the gut is a rapidly growing field, and the IESC niche is at the forefront of host-microbe activity to control nutrient absorption, endocrine signaling, energy homeostasis, immune response, and systemic health.

scholarly journals Gut Microbiota and Iron: The Crucial Actors in Health and Disease

2018 ◽  
Vol 11 (4) ◽  
pp. 98 ◽  
Author(s):  
Bahtiyar Yilmaz ◽  
Hai Li
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Life Forms ◽  
Iron Availability ◽  
Human Beings ◽  
Human Gastrointestinal Tract ◽  
Dynamic Modulation ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions

Iron (Fe) is a highly ample metal on planet earth (~35% of the Earth’s mass) and is particularly essential for most life forms, including from bacteria to mammals. Nonetheless, iron deficiency is highly prevalent in developing countries, and oral administration of this metal is so far the most effective treatment for human beings. Notably, the excessive amount of unabsorbed iron leave unappreciated side effects at the highly interactive host–microbe interface of the human gastrointestinal tract. Recent advances in elucidating the molecular basis of interactions between iron and gut microbiota shed new light(s) on the health and pathogenesis of intestinal inflammatory diseases. We here aim to present the dynamic modulation of intestinal microbiota by iron availability, and conversely, the influence on dietary iron absorption in the gut. The central part of this review is intended to summarize our current understanding about the effects of luminal iron on host–microbe interactions in the context of human health and disease.

scholarly journals Gut Microbiota and Mucosal Immunity in the Neonate

2018 ◽  
Vol 6 (3) ◽  
pp. 56 ◽  
Author(s):  
Majda Dzidic ◽  
Alba Boix-Amorós ◽  
Marta Selma-Royo ◽  
Alex Mira ◽  
Maria Collado
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
System Response ◽  
Delivery Mode ◽  
Complex Dynamic ◽  
Close Relationship ◽  
Gut Immunity ◽  
Microbe Interactions ◽  
Immune System Response ◽  
Host Microbe Interactions

Gut microbiota colonization is a complex, dynamic, and step-wise process that is in constant development during the first years of life. This microbial settlement occurs in parallel with the maturation of the immune system, and alterations during this period, due to environmental and host factors, are considered to be potential determinants of health-outcomes later in life. Given that host–microbe interactions are mediated by the immune system response, it is important to understand the close relationship between immunity and the microbiota during birth, lactation, and early infancy. This work summarizes the evidence to date on early gut microbiota colonization, and how it influences the maturation of the infant immune system and health during the first 1000 days of life. This review will also address the influence of perinatal antibiotic intake and the importance of delivery mode and breastfeeding for an appropriate development of gut immunity.

scholarly journals Introduction to the human gut microbiota

2017 ◽  
Vol 474 (11) ◽  
pp. 1823-1836 ◽  
Author(s):  
Elizabeth Thursby ◽  
Nathalie Juge
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Intestinal Bacteria ◽  
Life Time ◽  
Gi Tract ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Dynamic Population

The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host–microbe interactions.

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