Genetically identical co-housed pigs as models for dietary studies of gut microbiomes

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Fang Yang ◽  
Nicholas Chia ◽  
Meredith Mazur ◽  
James Pettigrew ◽  
Lawrence B. Schook ◽  
...  

AbstractThe impact of diet on the microbial composition in the gastrointestinal tract (GIT) has been well documented. However, quantifying the role of the diet in shaping microbial composition in humans has been difficult due to the influence of host genetics and the environment. To test the influence of diets on the GIT microbiome independently of host genotype and environment, two genetically identical co-housed pigs were used in an A-B-A-B design across four 14-day periods using two distinct diets that differed in dietary fiber source, soybean hulls or wheat bran. Shifts in fecal microbiomes were assessed with respect to dietary changes by 454-pyrosequencing analysis using the V3 region of the 16S rRNA genes. Similarity analysis revealed that the GIT microbiome distinctly clustered by diets rather than by individual. Diversity analysis showed that the diet fed had an influence on GIT microbiome diversity, which was host specific. While many bacterial taxa and KEGG orthologs reacted similarly to switches in diet, some bacterial taxa and KEGG orthologs reacted differentially in each of the pigs. While diet changed the GIT microbiome composition of isogenic co-housed pigs, inter-individual variations from epigenetics were not entirely eliminated by the use of cloned pigs.

2006 ◽  
Vol 73 (4) ◽  
pp. 1136-1145 ◽  
Author(s):  
Elina Vihavainen ◽  
Hanna-Saara Lundstr�m ◽  
Tuija Susiluoto ◽  
Joanna Koort ◽  
Lars Paulin ◽  
...  

ABSTRACT Some psychrotrophic lactic acid bacteria (LAB) are specific meat spoilage organisms in modified-atmosphere-packaged (MAP), cold-stored meat products. To determine if incoming broilers or the production plant environment is a source of spoilage LAB, a total of 86, 122, and 447 LAB isolates from broiler carcasses, production plant air, and MAP broiler products, respectively, were characterized using a library of HindIII restriction fragment length polymorphism (RFLP) patterns of the 16 and 23S rRNA genes as operational taxonomic units in numerical analyses. Six hundred thirteen LAB isolates from the total of 655 clustered in 29 groups considered to be species specific. Sixty-four percent of product isolates clustered either with Carnobacterium divergens or with Carnobacterium maltaromaticum type strains. The third major product-associated cluster (17% of isolates) was formed by unknown LAB. Representative strains from these three clusters were analyzed for the phylogeny of their 16S rRNA genes. This analysis verified that the two largest RFLP clusters consisted of carnobacteria and showed that the unknown LAB group consisted of Lactococcus spp. No product-associated LAB were detected in broiler carcasses sampled at the beginning of slaughter, whereas carnobacteria and lactococci, along with some other specific meat spoilage LAB, were recovered from processing plant air at many sites. This study reveals that incoming broiler chickens are not major sources of psychrotrophic spoilage LAB, whereas the detection of these organisms from the air of the processing environment highlights the role of processing facilities as sources of LAB contamination.


2021 ◽  
Author(s):  
E. D. Baranova ◽  
V. G. Druzhinin ◽  
L. V. Matskova ◽  
P. S. Demenkov ◽  
V. P . Volobaev ◽  
...  

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.


2003 ◽  
Vol 69 (10) ◽  
pp. 6056-6063 ◽  
Author(s):  
Anushree Malik ◽  
Masashi Sakamoto ◽  
Shohei Hanazaki ◽  
Masamitsu Osawa ◽  
Takanori Suzuki ◽  
...  

ABSTRACT Thirty-two strains of nonflocculating bacteria isolated from sewage-activated sludge were tested by a spectrophotometric assay for their ability to coaggregate with one other in two-membered systems. Among these strains, eight showed significant (74 to 99%) coaggregation with Acinetobacter johnsonii S35 while only four strains coaggregated, to a lesser extent (43 to 65%), with Acinetobacter junii S33. The extent and pattern of coaggregation as well as the aggregate size showed good correlation with cellular characteristics of the coaggregating partners. These strains were identified by sequencing of full-length 16S rRNA genes. A. johnsonii S35 could coaggregate with strains of several genera, such as Oligotropha carboxidovorans, Microbacterium esteraromaticum, and Xanthomonas spp. The role of Acinetobacter isolates as bridging organisms in multigeneric coaggregates is indicated. This investigation revealed the role of much-neglected nonflocculating bacteria in floc formation in activated sludge.


2020 ◽  
Vol 75 (6) ◽  
pp. 577-584
Author(s):  
G. R. Bikbavova ◽  
M. A. Livzan

In recent decades, an increase in the incidence of ulcerative colitis has been observed throughout the world. The purpose of this review is to generalize the available information on the influence of environmental factors and intestinal microbiome on the occurrence and development of ulcerative colitis, the role of bacteria metabolism products in the pathogenesis of the disease. Studied literature, we came to the conclusion that lifestyle in the era of post-industrial society has a significant impact on the microbial composition of the intestine and leads to changes in its diversity in patients suffering from ulcerative colitis. The changes include a decrease in the number of residential flora with anti-inflammatory activity, which synthesize short-chain fatty acids, and an increase in the number of potentially pathogenic and pathogenic microorganisms. Within the phylums Firmicutes and Proteobacteria, the proportional ratio changes. The combination of aggression factors (deterioration of the intestinal microbiome composition, the presence of aggressive intestinal metabolites) leads to intestinal mucosa permeability disfunction, impairing its barrier function. Food and bacterial agents can penetrate deeper layers of the intestinal wall through mucosal defects, which then stimulate the development of inflammatory and immune responses.


Pathogens ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 35 ◽  
Author(s):  
Marzia Vergine ◽  
Joana B. Meyer ◽  
Massimiliano Cardinale ◽  
Erika Sabella ◽  
Martin Hartmann ◽  
...  

Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.


2000 ◽  
Vol 66 (6) ◽  
pp. 2578-2588 ◽  
Author(s):  
G. W. Tannock ◽  
K. Munro ◽  
H. J. M. Harmsen ◽  
G. W. Welling ◽  
J. Smart ◽  
...  

ABSTRACT The composition of the fecal microflora of 10 healthy subjects was monitored before (6-month control period), during (6-month test period), and after (3-month posttest period) the administration of a milk product containing Lactobacillus rhamnosus DR20 (daily dose, 1.6 × 109 lactobacilli). Monthly fecal samples were examined by a variety of methods, including bacteriological culture analysis, fluorescent in situ hybridization with group-specific DNA probes, denaturing gradient gel electrophoresis of the V2-V3 region of 16S rRNA genes amplified by PCR, gas-liquid chromatography, and bacterial enzyme activity analysis. The composition of theLactobacillus population of each subject was analyzed by pulsed-field gel electrophoresis of bacterial DNA digests in order to differentiate between DR20 and other strains present in the samples. Representative isolates of lactobacilli were identified to the species level by sequencing the V2-V3 region of their 16S rRNA genes and comparing the sequences obtained (BLAST search) to sequences in the GenBank database. DR20 was detected in the feces of all of the subjects during the test period, but at different frequencies. The presence of DR20 among the numerically predominant strains was related to the presence or absence of a stable indigenous population of lactobacilli during the control period. Strain DR20 did not persist at levels of >102 cells per g in the feces of most of the subjects after consumption of the product ceased; the only exception was one subject in which this strain was detected for 2 months during the posttest period. We concluded that consumption of the DR20-containing milk product transiently altered the Lactobacillus and enterococcal contents of the feces of the majority of consumers without markedly affecting biochemical or other bacteriological factors.


2020 ◽  
Author(s):  
Lucian Staicu ◽  
Mikolaj Dziurzynski ◽  
Adrian Gorecki ◽  
Gavin Collins ◽  
Simon Mills ◽  
...  

<p>Selenium (Se) is one of the latest chemical elements identified as a terminal electron acceptor in anaerobic respiration. Before this important discovery, Se was mainly known for its toxicity and its limited use as an essential element for microbial metabolism (Staicu et al., 2019). This study screened the presence of selenium respiratory genes/operons and the impact of selenium on the microbial community from a methanogenic anaerobic granular sludge. The inoculum was collected from a full-scale bioreactor treating dairy wastewater (Ireland). To identify the presence of selenium respiration, the following primers were designed: for selenate, SeO<sub>4</sub><sup>2-</sup> (Thauera selenatis, Bacillus selenatarsenatis SF-1) and for selenite, SeO<sub>3</sub><sup>2-</sup> (Bacillus selenitireducens MLS10). The primers were designed based on the available sequences and refined using the UniPriVal algorithm developed by our group at University of Warsaw. Apart from Se respiration, the study also investigated the change in bacterial diversity using 16S rRNA genes as a function of incubation time and exposure to selenate (with acetate as electron donor) and selenite (with lactate as e-donor). An additional focus of the study attempted to shed light into the biomineralization of elemental Se, Se<sup>0</sup>, since this process is still not fully understood (e.g. intracellular vs extracellular nucleation, growth of the particles by an Ostwald-like ripening process) (Staicu and Barton, 2017). The results indicate the high contribution of Archaea (22% - 37%) to the community of the granular sludge. The addition of 10 mM selenate/selenite did not have an impact on the Archaean community, nor did it trigger the reduction of selenate/selenite to Se<sup>0</sup> via a known respiratory pathway. On the other hand, selenium addition did not particularly affect the community structure. There was a shift towards Bacteroidetes during the 7-day incubation period, with a high and consistent contribution of Firmicutes over Bacilli, which are putative host of selenate and selenite reductases. Furthermore, no significant Betaproteobacteria (Thauera selenatis) were identified, other putative host of selenate reductase. The biogenic Se<sup>0</sup> particles were localized both outside and at the intracellular level, displaying polydisperse size distribution (<100-500 nm), indicative of different biomineralization mechanisms involved. Overall, this dataset indicates the reduction of selenium might be a purely detoxification process in methanogenic Archaea-dominated microbial communities, which brings into question the use of high energy-dense selenium oxyanions for respiratory purposes in certain biogeochemical conditions. Alternatively, this might emphasize the uncharted respiratory potential of selenium, since the process was reported to have diverse ecosystem distribution (Steinberg and Oremland, 1990).</p> <p><strong>Reference</strong></p> <p>Staicu LC, Barton LL (2017) Microbial metabolism of selenium – for survival or profit. In: Bioremediation of selenium contaminated wastewaters, van Hullebusch ED (Ed.), Springer, 1-31.</p> <p>Staicu LC, Simon S, Guibaud G et al. (2019) Biogeochemistry of trace elements in anaerobic digesters. In: Trace elements in anaerobic biotechnologies, Fermoso FF et al. (Eds.), IWA, 23-50.</p> <p>Steinberg NA, Oremland RS (1990) Dissimilatory selenate reduction potentials in a diversity of sediment types. Appl Environ Microbiol 56, 3550-57.</p>


2017 ◽  
Vol 50 (6) ◽  
pp. 1600746 ◽  
Author(s):  
Alexandra Zimmermann ◽  
Henrik Knecht ◽  
Robert Häsler ◽  
Gernot Zissel ◽  
Karoline I. Gaede ◽  
...  

Sarcoidosis is a granulomatous disease that mainly affects the lung. A role of microbial factors in disease pathogenesis is assumed, but has not been investigated systematically in a large cohort.This cross-sectional study compared the lung microbiota of 71 patients with sarcoidosis, 15 patients with idiopathic pulmonary fibrosis (non-infectious controls) and 10 healthy controls (HCs). Next-generation sequencing of 16S DNA was used on bronchoalveolar lavage samples to characterise the microbial composition, which was analysed for diversity and indicator species. Host genotypes for 13 known sarcoidosis risk variants were determined and correlated with microbial parameters.The microbial composition differed significantly between sarcoidosis and HC samples (redundancy analysis ANOVA, p=0.025) and between radiographic Scadding types. Atopobium spp. was detected in 68% of sarcoidosis samples, but not in HC samples. Fusobacterium spp. was significantly more abundant in sarcoidosis samples compared with those from HCs. Mycobacteria were found in two of 71 sarcoidosis samples. Host-genotype analysis revealed an association of the rs2076530 (BTNL2) risk allele with a decrease in bacterial burden (p=0.002).Our results indicate Scadding type-dependent microbiota in sarcoidosis BAL samples. Atopobium spp. and Fusobacterium spp. were identified as sarcoidosis-associated bacteria, which may enable new insights into the pathogenesis and treatment of the disease.


Atmosphere ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 45
Author(s):  
Angelina Metaxatos ◽  
Sydonia Manibusan ◽  
Gediminas Mainelis

We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.


2021 ◽  
Vol 16 (3) ◽  
pp. 26-32
Author(s):  
A. S. Khudovekova ◽  
Ya. A. Rudenko ◽  
A. E. Dorosevich

Multiple myeloma is a tumor of plasma cells, one of the most common malignant blood diseases. It is preceded by a stage called monoclonal gammopathy of undetermined significance, from which true multiple myeloma develops in only a small percentage of cases. It was assumed that this process is associated with the accumulation of genetic mutations, but in recent years there is increasing evidence that the bone marrow microenvironment plays a key role in progression and that it can become a target for therapy that prevents the myeloma development. The review considers the role of mesenchymal stem cells, immune system cells, endotheliocytes, fibroblasts, adipocytes, osteoclasts and osteoblasts in multiple myeloma progression, as well as the impact of the sympathetic nervous system and microbiome composition.


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