scholarly journals Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range predictions

Author(s):  
Andrew J. Hryckowian ◽  
Bryan D. Merrill ◽  
Nathan T. Porter ◽  
William Van Treuren ◽  
Eric J. Nelson ◽  
...  

SummaryOur emerging view of the gut microbiome largely focuses on bacteria and less is known about other microbial components such as of bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut’s “viral dark matter” and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.

2018 ◽  
Vol 85 (10) ◽  
Author(s):  
Alli Lynch ◽  
Seshu R. Tammireddy ◽  
Mary K. Doherty ◽  
Phillip D. Whitfield ◽  
David J. Clarke

ABSTRACTAcylated amino acids function as important components of the cellular membrane in some bacteria. Biosynthesis is initiated by theN-acylation of the amino acid, and this is followed by subsequentO-acylation of the acylated molecule, resulting in the production of the mature diacylated amino acid lipid. In this study, we use both genetics and liquid chromatography-mass spectrometry (LC-MS) to characterize the biosynthesis and function of a diacylated glycine lipid (GL) species produced inBacteroides thetaiotaomicron. We, and others, have previously reported the identification of a gene, namedglsBin this study, that encodes anN-acyltransferase activity responsible for the production of a monoacylated glycine calledN-acyl-3-hydroxy-palmitoyl glycine (or commendamide). In all of theBacteroidalesgenomes sequenced so far, theglsBgene is located immediately downstream from a gene, namedglsA, that is also predicted to encode a protein with acyltransferase activity. We use LC-MS to show that the coexpression ofglsBandglsAresults in the production of GL inEscherichia coli. We constructed a deletion mutant of theglsBgene inB. thetaiotaomicron, and we confirm thatglsBis required for the production of GL inB. thetaiotaomicron. Moreover, we show thatglsBis important for the ability ofB. thetaiotaomicronto adapt to stress and colonize the mammalian gut. Therefore, this report describes the genetic requirements for the biosynthesis of GL, a diacylated amino acid species that contributes to fitness in the human gut bacteriumB. thetaiotaomicron.IMPORTANCEThe gut microbiome has an important role in both health and disease of the host. The mammalian gut microbiome is often dominated by bacteria from theBacteroidales, an order that includesBacteroidesandPrevotella. In this study, we have identified an acylated amino acid, called glycine lipid, produced byBacteroides thetaiotaomicron, a beneficial bacterium originally isolated from the human gut. In addition to identifying the genes required for the production of glycine lipids, we show that glycine lipids have an important role during the adaptation ofB. thetaiotaomicronto a number of environmental stresses, including exposure to either bile or air. We also show that glycine lipids are important for the normal colonization of the murine gut byB. thetaiotaomicron. This work identifies glycine lipids as an important fitness determinant inB. thetaiotaomicronand therefore increases our understanding of the molecular mechanisms underpinning colonization of the mammalian gut by beneficial bacteria.


Author(s):  
Giorgio Casaburi ◽  
Rebbeca Duar ◽  
Heather K. Brown ◽  
Ryan Mitchell ◽  
Sufyan Kazi ◽  
...  

1981 ◽  
Vol 59 (9) ◽  
pp. 1836-1846 ◽  
Author(s):  
Murray J. Kennedy

Previous experimental and field studies have shown that variations within the genus Haematoloechus may result from differences in age and degree of maturity, extent of crowding, species of host, and other factors.Based on these observations, only 6 of the 15 previously known species from Canada and the United States are considered valid. The valid species and their synonyms are as follows: Haematoloechus longiplexus Stafford, 1902; H. breviplexus Stafford, 1902; H. varioplexus Stafford, 1902 (= H. parviplexus, = H. buttensis, = H. similiplexus, = H. floedae, and H. uniplexus); H. kernensis Ingles, 1932 (= H. tumidus); H. medioplexus Stafford, 1902; and H. complexus (Seely, 1906) (= H. coloradensis, = H. confusus, = H. oxyorchis).The existence of three species groups is hypothesized. Haematoloechus longiplexus and H. breviplexus constitute one group, characterized by little geographical variation and a narrow host range. They are typically parasites of Rana catesbeiana and R. clamitans. Haematoloechus varioplexus and H. kernensis constitute the second group. These species have a wider host range and greater variation in characters purported to be specific differences. The third group includes those lung flukes which do not contain extracaecal loops (H. medioplexus and H. complexus). Of these, only H. medioplexus had little geographical variation and was found to occur in a single frog host.


2017 ◽  
Vol 84 (5) ◽  
Author(s):  
M. Andrea Azcarate-Peril ◽  
Natasha Butz ◽  
Maria Belen Cadenas ◽  
Matthew Koci ◽  
Anne Ballou ◽  
...  

ABSTRACT Salmonella is estimated to cause one million foodborne illnesses in the United States every year. Salmonella -contaminated poultry products are one of the major sources of salmonellosis. Given the critical role of the gut microbiota in Salmonella transmission, a manipulation of the chicken intestinal microenvironment could prevent animal colonization by the pathogen. In Salmonella , the global regulator gene fnr ( f umarate n itrate r eduction) regulates anaerobic metabolism and is essential for adapting to the gut environment. This study tested the hypothesis that an attenuated Fnr mutant of Salmonella enterica serovar Typhimurium (attST) or prebiotic galacto-oligosaccharides (GOS) could improve resistance to wild-type Salmonella via modifications to the structure of the chicken gut microbiome. Intestinal samples from a total of 273 animals were collected weekly for 9 weeks to evaluate the impact of attST or prebiotic supplementation on microbial species of the cecum, duodenum, jejunum, and ileum. We next analyzed changes to the gut microbiome induced by challenging the animals with a wild-type Salmonella serovar 4,[5],12:r:− (Nal r ) strain and determined the clearance rate of the virulent strain in the treated and control groups. Both GOS and the attenuated Salmonella strain modified the gut microbiome but elicited alterations of different taxonomic groups. The attST produced significant increases of Alistipes and undefined Lactobacillus , while GOS increased Christensenellaceae and Lactobacillus reuteri . The microbiome structural changes induced by both treatments resulted in a faster clearance after a Salmonella challenge. IMPORTANCE With an average annual incidence of 13.1 cases/100,000 individuals, salmonellosis has been deemed a nationally notifiable condition in the United States by the Centers for Disease Control and Prevention (CDC). Earlier studies demonstrated that Salmonella is transmitted by a subset of animals (supershedders). The supershedder phenotype can be induced by antibiotics, ascertaining an essential role for the gut microbiota in Salmonella transmission. Consequently, modulation of the gut microbiota and modification of the intestinal microenvironment could assist in preventing animal colonization by the pathogen. Our study demonstrated that a manipulation of the chicken gut microbiota by the administration of an attenuated Salmonella strain or prebiotic galacto-oligosaccharides (GOS) can promote resistance to Salmonella colonization via increases of beneficial microorganisms that translate into a less hospitable gut microenvironment.


PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e53838 ◽  
Author(s):  
Audrie Lin ◽  
Elisabeth M. Bik ◽  
Elizabeth K. Costello ◽  
Les Dethlefsen ◽  
Rashidul Haque ◽  
...  

2018 ◽  
Author(s):  
Andrew W. Brooks ◽  
Sambhawa Priya ◽  
Ran Blekhman ◽  
Seth R. Bordenstein

AbstractComposed of hundreds of microbial species, the composition of the human gut microbiota can vary with chronic diseases underlying health disparities that disproportionally affect ethnic minorities. However, the influence of ethnicity on the gut microbiota remains largely unexplored and lacks reproducible generalizations across studies. By distilling associations between ethnicity and differences in two United States based 16S gut microbiota datasets including 1,673 individuals, we report 12 microbial genera and families that reproducibly vary by ethnicity. Interestingly, a majority of these microbial taxa, including the most heritable bacterial family, Christensenellaceae, overlap with genetically-associated taxa and form co-occurring clusters linked by similar fermentative and methanogenic metabolic processes. These results demonstrate recurrent associations between specific taxa in the gut microbiota and ethnicity, providing hypotheses for examining specific members of the gut microbiota as mediators of health disparities.


EDIS ◽  
2006 ◽  
Vol 2006 (7) ◽  
Author(s):  
Jamba Gyeltshen ◽  
Amanda Hodges

The twobanded Japanese weevil, Pseudocneorhinus bifasciatus (Roelofs), first collected in the United States in 1914 near Philadelphia, was most likely introduced with infested nursery stock from Japan (Wheeler and Boyd 2005). With a host range of over 100 plant species, the twobanded Japanese weevil is recognized in the northeastern and midwestern United States as an important pest of landscape plantings (Wheeler and Boyd 2005). Although not a pest of major concern yet in the southeastern states, it is likely to extend its range due to movement of nursery stock. In July 2005, two specimens of the twobanded Japanese weevil were collected at Chipley, Florida, which is in Washington county (Thomas 2005). This document is EENY-361 (IN646), one of a series of the Entomology and Nematology Department, UF/IFAS Extension. Original publication date December 2005. EENY361/IN646: Twobanded Japanese Weevil, Pseudocneorhinus bifasciatus Roelofs (Insecta: Coleoptera: Curculionidae) (ufl.edu)


Subject China's space warfare capabilities. Significance China on December 17 launched a satellite that will test a new method for detecting dark matter -- the first of a series of five missions that put China at the cutting edge of space science. Separately, Beijing and Washington last month set up a 'space hotline' to reduce the risk of conflict in space -- an agreement representing acknowledgement of China's space capabilities and the challenge they pose to US strategic and tactical superiority. Impacts China still lags the United States significantly, but is eroding US dominance. Space capabilities will be integral to the success of China's 'anti-access/area denial' strategy. Earth observation and navigation satellites will support civilian enforcement of China's maritime claims. China will seek space collaboration with other developing countries.


2020 ◽  
Vol 21 (1) ◽  
pp. 19-20
Author(s):  
Mattie M. Baumann ◽  
Roy G. Kiambi ◽  
Benham E. Lockhart

The lady’s slipper orchids are a subfamily encompassing over 160 species, including the state flower of Minnesota, Cypripedium reginae. Hydrangea is a genus of about 75 species of shrubs and trees that are popular in perennial gardens. Chlorotic and necrotic foliar symptoms were observed in lady’s slipper orchid and Hydrangea arborescens on plants in St. Paul, Minnesota. From partially purified extracts, virus particles resembling those of tobacco rattle virus (TRV) were observed. TRV-specific primers amplified products from both hydrangea and lady’s slipper and were then sequenced. The sequences matched published TRV sequences with 99% identity, confirming the presence of the virus. TRV has a broad host range including ornamental, vegetable, and weed hosts. This is the first report of TRV infection in both lady’s slipper and hydrangea in Minnesota and the United States.


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