Microbiomes of Unreactive and Pathologically Altered Ileocecal Lymph Nodes of Slaughter Pigs

ABSTRACTMicrobe-laden dendritic cells are shifted to ileocecal lymph nodes (ICLNs), where microbes are concentrated and an adequate immune response is triggered. Hence, ICLNs are at a crucial position in immune anatomy and control processes of the local immune system. Pathological alterations in ICLNs, such as reactive hyperplasia,lymphadenitis purulenta, orgranulomatosa, can harbor a multitude of pathogens and commensals, posing a potential zoonotic risk in animal production. The aim of this study was to characterize the microbial diversity of unreactive ICLNs of slaughter pigs and to investigate community shifts in reactive ICLNs altered by enlargement, purulence, or granulomatous formations. Pyrosequencing of 16S rRNA gene amplicons from 32 ICLNs yielded 175,313 sequences, clustering into 650 operational taxonomic units (OTUs). OTUs were assigned to 239 genera and 11 phyla. Besides a highly diverse bacterial community in ICLNs, we observed significant shifts in pathologically altered ICLNs. The relative abundances ofCloacibacterium- andNovosphingobium-associated OTUs and the genusFaecalibacteriumwere significantly higher in unreactive ICLNs than in pathologically altered ICLNs. Enlarged ICLNs harbored significantly moreLactobacillus- andClostridium-associated sequences. Relative abundances ofMycoplasma,Bacteroides,Veillonella, andVariovoraxOTUs were significantly increased in granulomatous ICLNs, whereas abundances ofPseudomonas,Escherichia, andAcinetobacterOTUs were significantly increased in purulent ICLNs (P< 0.05). Correlation-based networks revealed interactions among OTUs in all ICLN groups, and discriminant analyses depicted discrimination in response to pathological alterations. This study is the first community-based survey in ICLNs of livestock animals and will provide a basis to broaden the knowledge of microbe-host interactions in pigs.

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Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

Applied and Environmental Microbiology ◽

10.1128/aem.03001-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 177-183 ◽

Cited By ~ 10

Author(s):

Lavane Kim ◽

Eulyn Pagaling ◽

Yi Y. Zuo ◽

Tao Yan

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Bacterial Species ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Content Type ◽

Property Change ◽

And Control ◽

Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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Quantifying the Survival of MultipleSalmonella entericaSerovarsIn Vivovia Massively Parallel Whole-Genome Sequencing To Predict Zoonotic Risk

Applied and Environmental Microbiology ◽

10.1128/aem.02262-17 ◽

2017 ◽

Vol 84 (4) ◽

Cited By ~ 4

Author(s):

Prerna Vohra ◽

Marie Bugarel ◽

Frances Turner ◽

Guy H. Loneragan ◽

Jayne C. Hope ◽

...

Keyword(s):

Lymph Nodes ◽

Genome Sequencing ◽

Lymphatic System ◽

Massively Parallel ◽

Whole Genome ◽

Content Type ◽

Peripheral Lymph ◽

Zoonotic Risk ◽

Mixed Populations

ABSTRACTSalmonella entericais an animal and zoonotic pathogen of worldwide importance.Salmonellaserovars that differ in their host and tissue tropisms exist. Cattle are an important reservoir of human nontyphoidal salmonellosis, and contaminated bovine peripheral lymph nodes enter the food chain via ground beef. The relative abilities of different serovars to survive within the bovine lymphatic system are poorly understood and constrain the development of control strategies. This problem was addressed by developing a massively parallel whole-genome sequencing method to study mixed-serovar infectionsin vivo.Salmonellaserovars differ genetically by naturally occurring single nucleotide polymorphisms (SNPs) in certain genes. It was hypothesized that these SNPs could be used as markers to simultaneously identify serovars in mixed populations and quantify the abundance of each member in a population. The performance of the method was validatedin vitrousing simulated pools containing up to 11 serovars in various proportions. It was then applied to study serovar survivalin vivoin cattle challenged orally with the same 11 serovars. All the serovars successfully colonized the bovine lymphatic system, including the peripheral lymph nodes, and thus pose similar risks of zoonosis. This method enables the fates of multiple genetically unmodified strains to be evaluated simultaneously in a single animal. It could be useful in reducing the number of animals required to study mixed-strain infections and in testing the cross-protective efficacy of vaccines and treatments. It also has the potential to be applied to diverse bacterial species which possess shared but polymorphic alleles.IMPORTANCEWhile someSalmonellaserovars are more frequently isolated from lymph nodes rather than the feces and environment of cattle, the relative abilities of serovars to survive within the lymphatic system of cattle remain ill defined. A sequencing-based method which used available information from sequencedSalmonellagenomes to study the dynamics of mixed-serovar infectionsin vivowas developed. The main advantages of the method include the simultaneous identification and quantification of multiple strains without any genetic modification and minimal animal use. This approach could be used in vaccination trials or in epidemiological surveys where an understanding of the dynamics of closely related strains of a pathogen in mixed populations could inform the prediction of zoonotic risk and the development of intervention strategies.

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Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation

Applied and Environmental Microbiology ◽

10.1128/aem.02955-13 ◽

2013 ◽

Vol 79 (24) ◽

pp. 7827-7836 ◽

Cited By ~ 107

Author(s):

Danilo Ercolini ◽

Erica Pontonio ◽

Francesca De Filippis ◽

Fabio Minervini ◽

Antonietta La Storia ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Microbial Ecology ◽

Denaturing Gradient Gel Electrophoresis ◽

Diversity Indices ◽

Rrna Gene ◽

Content Type ◽

Gradient Gel Electrophoresis ◽

Plate Counts ◽

Relative Abundances

ABSTRACTThe bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between lactic acid bacteria and yeasts, the rate of acidification, a permutation analysis based on biochemical and microbial features, the number of operational taxonomic units (OTUs), and diversity indices all together demonstrated the maturity of the sourdoughs during 5 to 7 days of propagation. Flours were mainly contaminated by metabolically active genera (Acinetobacter,Pantoea,Pseudomonas,Comamonas,Enterobacter,Erwinia, andSphingomonas) belonging to the phylumProteobacteriaorBacteroidetes(genusChryseobacterium). Their relative abundances varied with the flour. Soon after 1 day of propagation, this population was almost completely inhibited except for theEnterobacteriaceae. Although members of the phylumFirmicuteswere present at very low or intermediate relative abundances in the flours, they became dominant soon after 1 day of propagation. Lactic acid bacteria were almost exclusively representative of theFirmicutesby this time.Weissellaspp. were already dominant in rye flour and stably persisted, though they were later flanked by theLactobacillus sakeigroup. There was a succession of species during 10 days of propagation of wheat sourdoughs. The fluctuation between dominating and subdominating populations ofL. sakeigroup,Leuconostocspp.,Weissellaspp., andLactococcus lactiswas demonstrated. Other subdominant species such asLactobacillus plantarumwere detectable throughout propagation. As shown by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis,Saccharomyces cerevisiaedominated throughout the sourdough propagation. Notwithstanding variations due to environmental and technology determinants, the results of this study represent a clear example of how the microbial ecology evolves during sourdough preparation.

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Microorganisms Move a Short Distance into an Almond Orchard from an Adjacent Upwind Poultry Operation

Applied and Environmental Microbiology ◽

10.1128/aem.00573-20 ◽

2020 ◽

Vol 86 (15) ◽

Author(s):

Christopher G. Theofel ◽

Thomas R. Williams ◽

Eduardo Gutierrez ◽

Gordon R. Davidson ◽

Michele Jay-Russell ◽

...

Keyword(s):

Relative Abundance ◽

Foodborne Pathogens ◽

Short Distance ◽

Soil Surface ◽

Plate Count ◽

Rrna Gene ◽

Content Type ◽

Aerobic Plate Count ◽

And Control ◽

Almond Orchard

ABSTRACT Over a 2-year period, drag swabs of orchard soil surface and air, soil, and almond leaf samples were collected in an almond orchard adjacent to (35 m from the first row of trees) and downwind from a poultry operation and in two almond orchards (controls) that were surrounded by other orchards. Samples were evaluated for aerobic plate count, generic Escherichia coli, other coliforms, the presence of Salmonella, bacterial community structure (analyzed through sequencing of the 16S rRNA gene), and amounts of dry solids (dust) on leaf surfaces on trees 0, 60, and 120 m into each orchard. E. coli was isolated from 41 of 206 (20%) and 1 of 207 (0.48%) air samples in the almond-poultry and control orchards, respectively. Salmonella was not isolated from any of the 529 samples evaluated. On average, the amount of dry solids on leaves collected from trees closest to the poultry operation was more than 2-fold greater than from trees 120 m into the orchard or from any of the trees in the control orchards. Members of the family Staphylococcaceae—often associated with poultry—were, on average, significantly (P < 0.001) more abundant in the phyllosphere of trees closest to the poultry operation (10% of relative abundance) than in trees 120 m into the orchard (1.7% relative abundance) or from any of the trees in control orchards (0.41% relative abundance). Poultry-associated microorganisms from a commercial operation transferred a short distance into an adjacent downwind almond orchard. IMPORTANCE The movement of microorganisms, including foodborne pathogens, from animal operations into adjacent plant crop-growing environments is not well characterized. This study provides evidence that dust and bioaerosols moved from a commercial poultry operation a short distance downwind into an almond orchard and altered the microbiome recovered from the leaves. These data provide growers with information they can use to assess food safety risks on their property.

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Duodenal-Mucosal Bacteria Associated with Celiac Disease in Children

Applied and Environmental Microbiology ◽

10.1128/aem.00869-13 ◽

2013 ◽

Vol 79 (18) ◽

pp. 5472-5479 ◽

Cited By ~ 79

Author(s):

Ester Sánchez ◽

Ester Donat ◽

Carmen Ribes-Koninckx ◽

Maria Leonor Fernández-Murga ◽

Yolanda Sanz

Keyword(s):

Celiac Disease ◽

Klebsiella Oxytoca ◽

16S Rrna Gene Sequencing ◽

Duodenal Mucosa ◽

Plate Count ◽

Rrna Gene ◽

Content Type ◽

Inflammatory Status ◽

And Control ◽

Active Disease

ABSTRACTCeliac disease (CD) is an immune-mediated enteropathy triggered by the ingestion of cereal gluten proteins. This disorder is associated with imbalances in the gut microbiota composition that could be involved in the pathogenesis of CD. The aim of this study was to characterize the composition and diversity of the cultivable duodenal mucosa-associated bacteria of CD patients and control children. Duodenal biopsy specimens from patients with active disease on a gluten-containing diet (n= 32), patients with nonactive disease after adherence to a gluten-free diet (n= 17), and controls (n= 8) were homogenized and plated on plate count agar, Wilkins-Chalgren agar, brain heart agar, or yeast, Casitone, and fatty acid agar. The isolates were identified by partial 16S rRNA gene sequencing. Renyi diversity profiles showed the highest diversity values for active CD patients, followed by nonactive CD patients and control individuals. Members of the phylumProteobacteriawere more abundant in patients with active CD than in the other child groups, while those of the phylumFirmicuteswere less abundant. Members of the familiesEnterobacteriaceaeandStaphylococcaceae, particularly the speciesKlebsiella oxytoca,Staphylococcus epidermidis, andStaphylococcus pasteuri, were more abundant in patients with active disease than in controls. In contrast, members of the familyStreptococcaceaewere less abundant in patients with active CD than in controls. Furthermore, isolates of theStreptococcus anginosusandStreptococcus mutansgroups were more abundant in controls than in both CD patient groups, regardless of inflammatory status. The findings indicated that the disease is associated with the overgrowth of possible pathobionts that exclude symbionts or commensals that are characteristic of the healthy small intestinal microbiota.

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Mycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.051979-0 ◽

2013 ◽

Vol 63 (Pt_12) ◽

pp. 4669-4674 ◽

Cited By ~ 13

Author(s):

Véronique Guérin-Faublée ◽

Jean-Pierre Flandrois ◽

Catherine Pichat ◽

Maria Laura Boschiroli ◽

Brigitte Lamy

Keyword(s):

Phylogenetic Analysis ◽

Lymph Nodes ◽

Type Species ◽

Rrna Genes ◽

Rrna Gene ◽

Ssu Rrna ◽

Gene Sequences ◽

Content Type ◽

Ssu Rrna Gene ◽

Link Type

Three independent strains of a rapidly growing, non-chromogenic member of the genus Mycobacterium were isolated from lymph nodes of French cattle. Identification of the isolates was carried out using a polyphasic approach. The nearly complete SSU rRNA gene sequences (>1200 bp) of the strains MLB-A23, MLB-A30 and MLB-A84T were identical. A phylogenetic analysis of these unique SSU rRNA gene sequences showed that these strains were most closely related to Mycobacterium intermedium . Further phylogenetic analysis based on concatenated sequences (2854 bp) of four housekeeping genes (hsp65, rpoB, sodA and tuf), the transfer–messenger RNA (tmRNA) and SSU rRNA genes indicated that these three strains represented a distinct species that shares a common ancestor with M. intermedium . Phylogenetic and phenotypic data strongly indicate that the strains MLB-A23, MLB-A30 and MLB-A84T belong to a novel mycobacterial species for which the name Mycobacterium bourgelatii sp. nov. is proposed. The type strain is MLB-A84T ( = CIP 110557T = DSM 45746T).

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High Prevalence of Enterocytozoon bieneusi in Asymptomatic Pigs and Assessment of Zoonotic Risk at the Genotype Level

Applied and Environmental Microbiology ◽

10.1128/aem.00807-14 ◽

2014 ◽

Vol 80 (12) ◽

pp. 3699-3707 ◽

Cited By ~ 48

Author(s):

Wei Zhao ◽

Weizhe Zhang ◽

Fengkun Yang ◽

Jianping Cao ◽

Hua Liu ◽

...

Keyword(s):

Opportunistic Pathogen ◽

Small Subunit ◽

Enterocytozoon Bieneusi ◽

Rrna Gene ◽

Ssu Rrna ◽

Content Type ◽

Zoonotic Risk ◽

High Prevalence ◽

Life Threatening ◽

Clinically Significant

ABSTRACTEnterocytozoon bieneusiis an emerging and clinically significant enteric parasite infecting humans and animals and can cause life-threatening diarrhea in immunocompromised people. Pigs are considered to be one of the main reservoir hosts ofE. bieneusibased on their high prevalence rates and zoonotic genotypes in pigs. As an opportunistic pathogen,E. bieneusiinfection of pigs can be inapparent, which leads to neglect in detecting this parasite in pigs and assessing the epidemiological role of pigs in the transmission of human microsporidiosis. In the present study, 95 healthy pigs aged 2 or 3 months were randomly selected from three areas in Heilongjiang Province, China.E. bieneusiisolates were identified and genotyped based on the small-subunit (SSU) rRNA and internal transcribed spacer (ITS) regions of the rRNA gene by PCR and sequencing. A high prevalence ofE. bieneusiwas observed, 83.2% (79/95) at the SSU rRNA locus versus 89.5% (85/95) at the ITS locus. Ten ITS genotypes were obtained, comprising six known genotypes—EbpA (n= 30), D (n= 19), H (n= 18), O (n= 11), CS-1 (n= 1), and LW1 (n= 1)—and four novel genotypes named HLJ-I to HLJ-IV; 70.6% (60/85) ofE. bieneusigenotypes were zoonotic (genotypes EbpA, D, and O). The findings of a high prevalence ofE. bieneusiin pigs and a large percentage of zoonotic genotypes indicate that pigs may play a role in the transmission ofE. bieneusito humans and may become an important source of water contamination in our investigated areas.

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Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure

Applied and Environmental Microbiology ◽

10.1128/aem.01071-12 ◽

2012 ◽

Vol 78 (20) ◽

pp. 7438-7446 ◽

Cited By ~ 110

Author(s):

Jeanette Berg ◽

Kristian K. Brandt ◽

Waleed A. Al-Soud ◽

Peter E. Holm ◽

Lars H. Hansen ◽

...

Keyword(s):

Bacterial Communities ◽

Metal Tolerance ◽

Bacterial Community Composition ◽

Community Response ◽

Leucine Incorporation ◽

Rrna Gene ◽

Sequence Information ◽

Content Type ◽

Relative Abundances ◽

The Impact

ABSTRACTToxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g−1) stemming from industrial contamination with CuSO4more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [3H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including theProteobacteria,Bacteroidetes,Verrumicrobia,Chloroflexi,WS3, andPlanctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, theActinobacteria, showed no response and members of theAcidobacteriashowed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.

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Complete Genome Sequences of Two T4-Like Escherichia coli Bacteriophages

Genome Announcements ◽

10.1128/genomea.00586-18 ◽

2018 ◽

Vol 6 (26) ◽

Cited By ~ 1

Author(s):

Ana Rita Costa ◽

Stan J. J. Brouns ◽

Franklin L. Nobrega

Keyword(s):

Escherichia Coli ◽

Complete Genome ◽

Genome Sequences ◽

Content Type ◽

Bacterial Diseases ◽

Host Interactions ◽

Potential Applications ◽

Genome Annotations ◽

And Control

Bacteriophages and their proteins have potential applications in biotechnology for the detection and control of bacterial diseases. Here, we describe the sequencing and genome annotations of two strictly virulent Escherichia coli bacteriophages that may be explored for biocontrol strategies and to expand the understanding of phage-host interactions.

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Identification of Salivary Microorganisms and Metabolites Associated with Halitosis

Metabolites ◽

10.3390/metabo11060362 ◽

2021 ◽

Vol 11 (6) ◽

pp. 362

Author(s):

Jae-kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Amplicon Sequencing ◽

Control Group ◽

Rrna Gene ◽

Control Groups ◽

Relative Abundances ◽

The Difference ◽

Oral Microbes ◽

And Control ◽

The 16S Rrna Gene ◽

Insight Into

Halitosis is mainly caused by the action of oral microbes. The purpose of this study was to investigate the differences in salivary microbes and metabolites between subjects with and without halitosis. Of the 52 participants, 22 were classified into the halitosis group by the volatile sulfur compound analysis on breath samples. The 16S rRNA gene amplicon sequencing and metabolomics approaches were used to investigate the difference in microbes and metabolites in saliva of the control and halitosis groups. The profiles of microbiota and metabolites were relatively different between the halitosis and control groups. The relative abundances of Prevotella, Alloprevotella, and Megasphaera were significantly higher in the halitosis group. In contrast, the relative abundances of Streptococcus, Rothia, and Haemophilus were considerably higher in the control group. The levels of 5-aminovaleric acid and n-acetylornithine were significantly higher in the halitosis group. The correlation between identified metabolites and microbiota reveals that Alloprevotella and Prevotella might be related to the cadaverine and putrescine pathways that cause halitosis. This study could provide insight into the mechanisms of halitosis.

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