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Article ; Online: Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

Medelin Ocejo / Beatriz Oporto / José Luis Lavín / Ana Hurtado

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) ...

Abstract	Abstract Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of bla OXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluating the Inclusion of Cold-Pressed Rapeseed Cake in the Concentrate for Dairy Cows upon Ruminal Biohydrogenation Process, Ruminal Microbial Community and Milk Production and Acceptability

Idoia Goiri / Izaro Zubiria / Jose Luís Lavín / Hanen Benhissi / Raquel Atxaerandio / Roberto Ruiz / Nerea Mandaluniz / Aser García-Rodríguez

Animals, Vol 11, Iss 2553, p

2021 Volume 2553

Abstract: The aim of this trial was to assess the effect of feeding a concentrate including cold-pressed rapeseed cake (CPRC) on productive performance, milk quality and its sensory properties, ruminal biohydrogenation, and bacterial communities. Eighteen cows ... ...

Abstract	The aim of this trial was to assess the effect of feeding a concentrate including cold-pressed rapeseed cake (CPRC) on productive performance, milk quality and its sensory properties, ruminal biohydrogenation, and bacterial communities. Eighteen cows were paired, and two experimental diets (control vs. CPRC) were distributed within the pair. Concentrates were iso-energetic and iso-proteic and contained similar amounts of fat. The average days in milk, milk yield, and body weight of the animals were (mean ± SD) 172 ± 112 d, 585 ± 26 kg, and 25.4 ± 6.2 kg/d, respectively. The experiment lasted for 10 wk. Feeding CPRC resulted in lower ruminal saturated ( p < 0.001) and higher monounsaturated ( p = 0.002) fatty acids. Feeding CPRC increased Ruminococcus , Prevotella , and Entodinium but decreased Blautia p-75-a5; undefined genera within orders Clostridiaceae and RF39 and within families Christensenellaceae, Lachnospiracease, and Ruminococcaceae; and fungi from the phylum neocallimastigomycota. The milk fatty acid profile was characterized by a lower n6:n3 ratio ( p = 0.028). Feeding CPRC did not affect the milk yield, milk quality, or fat corrected milk ( p > 0.05). Feeding CPRC improved the overall milk acceptability ( p = 0.047). In conclusion, CPRC affected some microbial taxa, modified the biohydrogenation process, and improved the milk fatty acid profile and consumer acceptance without detrimental effects on milk production and composition.
Keywords	oilseed ; alternative feedstuffs ; palm oil ; soybean meal ; dairy cattle ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression

Ainize Peña-Cearra / Deguang Song / Janire Castelo / Ainhoa Palacios / Jose Luis Lavín / Mikel Azkargorta / Felix Elortza / Miguel Fuertes / Miguel Angel Pascual-Itoiz / Diego Barriales / Itziar Martín-Ruiz / Asier Fullaondo / Ana M. Aransay / Hector Rodríguez / Noah W. Palm / Juan Anguita / Leticia Abecia

npj Biofilms and Microbiomes, Vol 9, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal ... ...

Abstract	Abstract Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal inflammation. We observed previously that mice deficient in the mitochondrial protein MCJ (Methylation-controlled J protein) exhibit increased susceptibility to DSS colitis. However, it is unclear whether this phenotype is primarily driven by MCJ−/− associated gut microbiota dysbiosis or by direct effects of MCJ-deficiency. Here, we demonstrate that fecal microbiota transplantation (FMT) from MCJ-deficient into germ-free mice was sufficient to confer increased susceptibility to colitis. Therefore, an FMT experiment by cohousing was designed to alter MCJ-deficient microbiota. The phenotype resulting from complex I deficiency was reverted by FMT. In addition, we determined the protein expression pathways impacted by MCJ deficiency, providing insight into the pathophysiology of IBD. Further, we used magnetic activated cell sorting (MACS) and 16S rRNA gene sequencing to characterize taxa-specific coating of the intestinal microbiota with Immunoglobulin A (IgA-SEQ) in MCJ-deficient mice. We show that high IgA coating of fecal bacteria observed in MCJ-deficient mice play a potential role in disease progression. This study allowed us to identify potential microbial signatures in feces associated with complex I deficiency and disease progression. This research highlights the importance of finding microbial biomarkers, which might serve as predictors, permitting the stratification of ulcerative colitis (UC) patients into distinct clinical entities of the UC spectrum.
Keywords	Microbial ecology ; QR100-130
Subject code	570
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mitochondrial complex I dysfunction alters the balance of soluble and membrane-bound TNF during chronic experimental colitis

Ainize Peña-Cearra / Miguel Angel Pascual-Itoiz / Jose Luis Lavín / Miguel Fuertes / Itziar Martín-Ruiz / Janire Castelo / Ainhoa Palacios / Diego Barriales / Asier Fullaondo / Ana M Aransay / Hector Rodríguez / Juan Anguita / Leticia Abecia

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 10

Abstract: Abstract Inflammatory bowel disease (IBD) is a complex, chronic, relapsing and heterogeneous disease induced by environmental, genomic, microbial and immunological factors. MCJ is a mitochondrial protein that regulates the metabolic status of macrophages ...

Abstract	Abstract Inflammatory bowel disease (IBD) is a complex, chronic, relapsing and heterogeneous disease induced by environmental, genomic, microbial and immunological factors. MCJ is a mitochondrial protein that regulates the metabolic status of macrophages and their response to translocated bacteria. Previously, an acute murine model of DSS-induced colitis showed increased disease severity due to MCJ deficiency. Unexpectedly, we now show that MCJ-deficient mice have augmented tumor necrosis factor α converting enzyme (TACE) activity in the context of chronic inflammation. This adaptative change likely affects the balance between soluble and transmembrane TNF and supports the association of the soluble form and a milder phenotype. Interestingly, the general shifts in microbial composition previously observed during acute inflammation were absent in the chronic model of inflammation in MCJ-deficient mice. However, the lack of the mitochondrial protein resulted in increased alpha diversity and the reduction in critical microbial members associated with inflammation, such as Ruminococcus gnavus, which could be associated with TACE activity. These results provide evidence of the dynamic metabolic adaptation of the colon tissue to chronic inflammatory changes mediated by the control of mitochondrial function.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data.

Maria Canive / Oscar González-Recio / Almudena Fernández / Patricia Vázquez / Gerard Badia-Bringué / José Luis Lavín / Joseba M Garrido / Ramón A Juste / Marta Alonso-Hearn

PLoS ONE, Vol 16, Iss 8, p e

2021 Volume 0256091

Abstract: Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with ... ...

Abstract	Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats

Ainize Peña-Cearra / Alejandro Belanche / Monika Gonzalez-Lopez / José Luis Lavín / Miguel Ángel Pascual-Itoiz / Elisabeth Jiménez / Héctor Rodríguez / Ana Mª. Aransay / Juan Anguita / David R. Yáñez-Ruiz / Leticia Abecia

Animal Microbiome, Vol 3, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Background The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripheral blood mononuclear ... ...

Abstract	Abstract Background The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripheral blood mononuclear cells (PBMC) bacterial DNA from goats supplemented or not in early life with rumen liquid transplantation. Results Most of the bacterial DNA associated to PBMC was identified predominantly as Proteobacteria (55%) followed by Firmicutes (24%), Bacteroidetes (11%) and Actinobacteria (8%). The predominant genera found in PBMC samples were Pseudomonas, Prevotella, Sphingomonas, Acinetobacter, Corynebacterium and Ruminococcus. Other genera such as Butyrivibrivio, Bifidobacterium, Dorea and Coprococcus were also present in lower proportions. Several species known as blood pathogens or others involved in gut homeostasis such as Faecalibacterium prausnitzii were also identified. However, the PBMC microbiome phylum composition differed from that in the colon of goats (P ≤ 0.001), where Firmicutes was the predominant phylum (83%). Although, rumen liquid administration in early-life altered bacterial community structure and increased Tlr5 expression (P = 0.020) in colon pointing to higher bacterial translocation, less than 8% of OTUs in colon were also observed in PBMCs. Conclusions Data suggest that in physiological conditions, PBMC microbiome differs from and is not affected by colon gut microbiota in small ruminants. Although, further studies with larger number of animals and covering other animal tissues are required, results point to a common circulating bacterial profile on mammals being phylum Proteobacteria, and genera Pseudomonas and Prevotella the most abundants. All suggest that PBMC microbiome in healthy ruminants could be implicated in homeostatic condition. This study expands our knowledge about PBMC microbiome contribution to health in farm animals.
Keywords	Blood immune cells ; Ruminants ; Immunoglobulins ; Translocation ; Veterinary medicine ; SF600-1100 ; Microbiology ; QR1-502
Subject code	610
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression

Maria Canive / Nora Fernandez-Jimenez / Rosa Casais / Patricia Vázquez / José Luis Lavín / José Ramón Bilbao / Cristina Blanco-Vázquez / Joseba M. Garrido / Ramón A. Juste / Marta Alonso-Hearn

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 14

Abstract: Abstract Although genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with the susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection, only a few functional mutations for bovine ... ...

Abstract	Abstract Although genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with the susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection, only a few functional mutations for bovine paratuberculosis (PTB) have been characterized. Expression quantitative trait loci (eQTLs) are genetic variants typically located in gene regulatory regions that alter gene expression in an allele-specific manner. eQTLs can be considered as functional links between genomic variants, gene expression, and ultimately phenotype. In the current study, peripheral blood (PB) and ileocecal valve (ICV) gene expression was quantified by RNA-Seq from fourteen Holstein cattle with no lesions and with PTB-associated histopathological lesions in gut tissues. Genotypes were generated from the Illumina LD EuroG10K BeadChip. The associations between gene expression levels (normalized read counts) and genetic variants were analyzed by a linear regression analysis using R Matrix eQTL 2.2. This approach allowed the identification of 192 and 48 cis-eQTLs associated with the expression of 145 and 43 genes in the PB and ICV samples, respectively. To investigate potential relationships between these cis-eQTLs and MAP infection, a case–control study was performed using the genotypes for all the identified cis-eQTLs and phenotypical data (histopathology, ELISA for MAP-antibodies detection, tissue PCR, and bacteriological culture) of 986 culled cows. Our results suggested that the heterozygous genotype in the cis-eQTL-rs43744169 (T/C) was associated with the up-regulation of the MDS1 and EVI1 complex (MECOM) expression, with positive ELISA, PCR, and bacteriological culture results, and with increased risk of progression to clinical PTB. As supporting evidence, the presence of the minor allele was associated with higher MECOM levels in plasma samples from infected cows and with increased MAP survival in an ex-vivo macrophage killing assay. Moreover, the presence of the two minor alleles in the ...
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Author Correction

Maria Canive / Nora Fernandez‑Jimenez / Rosa Casais / Patricia Vázquez / José Luis Lavín / José Ramón Bilbao / Cristina Blanco‑Vázquez / Joseba M. Garrido / Ramón A. Juste / Marta Alonso‑Hearn

Scientific Reports, Vol 11, Iss 1, Pp 1-

Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression

2021 Volume 1

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Nature Portfolio
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Article ; Online: Effect of Feeding Cold-Pressed Sunflower Cake on Ruminal Fermentation, Lipid Metabolism and Bacterial Community in Dairy Cows

Izaro Zubiria / Aser Garcia-Rodriguez / Raquel Atxaerandio / Roberto Ruiz / Hanen Benhissi / Nerea Mandaluniz / Jose Luis Lavín / Leticia Abecia / Idoia Goiri

Animals, Vol 9, Iss 10, p

2019 Volume 755

Abstract: Cold-pressed sunflower cake (CPSC), by-product of oil-manufacturing, has high crude fat and linoleic acid concentrations, being a promising supplement to modulate rumen fatty acid (FA) profile. This trial studied CPSC effects on ruminal fermentation, ... ...

Abstract	Cold-pressed sunflower cake (CPSC), by-product of oil-manufacturing, has high crude fat and linoleic acid concentrations, being a promising supplement to modulate rumen fatty acid (FA) profile. This trial studied CPSC effects on ruminal fermentation, biohydrogenation and the bacterial community in dairy cows. Ten cows were used in a crossover design with two experimental diets and fed during two 63-day periods. The cows were group fed forage ad libitum and the concentrate individually. The concentrates, control and CPSC, were isoenergetic, isoproteic and isofat. The ruminal samples collected at the end of each experimental period were analyzed for short-chain fatty acid, FA and DNA sequencing. CPSC decreased butyrate molar proportion (4%, p = 0.005). CPSC decreased C16:0 (28%, p < 0.001) and increased C18:0 (14%, p < 0.001) and total monounsaturated FA, especially C18:1 trans-11 (13%, p = 0.023). The total purine derivative excretion tended to be greater (5%, p = 0.05) with CPSC, resulting in a 6% greater daily microbial N flow. CPSC did not affect the diversity indices but increased the relative abundances of Treponema and Coprococcus , and decreased Enterococcus , Ruminococcus and Succinivibrio . In conclusion, the changes in ruminal fermentation and the FA profile were not associated with changes in microbial diversity or abundance of dominant populations, however, they might be associated with less abundant genera.
Keywords	biohydrogenation ; sunflower cake ; microbiota ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes

Idoia Goiri / Xabier Díaz de Otálora / Roberto Ruiz / Jagoba Rey / Raquel Atxaerandio / Jose Luis Lavín / David San Martin / Mikel Orive / Bruno Iñarra / Jaime Zufia / Jabi Urkiza / Aser García-Rodríguez

Microorganisms, Vol 8, Iss 1961, p

2020 Volume 1961

Abstract: Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental ... ...

Abstract	Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental treatments (0, 30, 50, and 100 g SCG/kg). Ruminal samples were collected on day 50. DNA was extracted and subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA genes. Bioinformatic analyses were performed using QIIME (v.1.9.0). SCG increased dose-dependently bacterial diversity and altered bacterial structure. Further, 60, 78, and 449 operational taxonomic unit (OUT) were different between control and 30, 50 and 100 g/kg SCG groups, respectively. Higher differences were observed between the control and 100 g/kg SCG group, where OTU of the genera Treponema , CF231 , Butyrivibrio , BF331 , Anaeroplasma , Blautia , Fibrobacter , and Clostridium were enriched with SCG. Correlations between volatile fatty acids (VFA) and bacterial taxa were sparser in the SCG groups and had little overlap. Certain bacterial taxa presented different signs of the correlation with VFA in SCG and control groups, but Butyrivibrio and Blautia consistently correlated with branched-chain VFA in all groups. SCG induced shifts in the ruminal bacterial community and altered the correlation networks among bacterial taxa and ruminal VFA.
Keywords	circular economy ; coffee by-products ; ruminal microbes ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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