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Article: Low-Level Tetracycline Resistance Gene

Pacífico, Cátia / Wösten, Marc M S M / Hilbert, Friederike

2023 Volume 12, Issue 3

Abstract: ... ...

Abstract	Campylobacter
Language	English
Publishing date	2023-02-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics12030426
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Article ; Online: Sigla storax (Liquidambar orientalis) mitigates in vitro methane production without disturbances in rumen microbiota and nutrient fermentation in comparison to monensin.

Demirtas, Ahu / Pacífico, Cátia / Gruber, Theresa / Chizzola, Remigius / Zebeli, Qendrim / Khiaosa-Ard, Ratchaneewan

Journal of applied microbiology

2023 Volume 134, Issue 8

Abstract: Aim: The aim of this study was to investigate the in vitro dose-dependent effects of sigla storax (Styrax liquidus) on rumen microbiota and rumen microbial fermentation in comparison to monensin as a positive control.: Methods and results: This study ...

Abstract	Aim: The aim of this study was to investigate the in vitro dose-dependent effects of sigla storax (Styrax liquidus) on rumen microbiota and rumen microbial fermentation in comparison to monensin as a positive control. Methods and results: This study was carried out using a rumen simulation model (Rusitec). Treatments consisted of no additive (control), 10 mg l-1 of monensin sodium salt, 100 mg l-1 (Low-Sigla), and 500 mg l-1 (High-Sigla) of sigla storax (n = 6/treatment). In addition to rumen fermentation characteristics, rumen microbial composition was investigated using 16S rRNA sequencing. The methane variables and the acetate to propionate ratio decreased in the both High-Sigla and monensin groups (P < 0.05). High-Sigla had no effect on ammonia, total SCFA and nutrition degradation, while monensin decreased these parameters (P < 0.05). Unlike monensin, the sigla storax treatments did not affect the alpha or beta diversity indexes of the microbiota. The relative abundance of Methanomethylophilaceae and Ruminococcaceae decreased with High-Sigla and monensin (P < 0.05), and Atopobiaceae and Eggerthellaceae decreased with the both doses of sigla storax as well as monensin treatments (P < 0.05). Syntrophococcus, DNF00809, and Kandleria were among the genera that most decreased with High-Sigla and monensin (Q < 0.07) and were strongly positively correlated with methane production (r = 0.52-0.56). Conclusions: The high dose of sigla storax (500 mg l-1) decreased methane in the rumen ecosystem without adverse effects on nutrient degradation and SCFA production, and without dramatically impacting the microbial composition. Sigla storax might be a novel feed additive to mitigate methane in cattle.
MeSH term(s)	Animals ; Cattle ; Monensin/pharmacology ; Monensin/metabolism ; Fermentation ; Liquidambar/metabolism ; Rumen/metabolism ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 16S/metabolism ; Styrax/metabolism ; Microbiota ; Methane/metabolism ; Nutrients ; Diet/veterinary ; Animal Feed
Chemical Substances	Monensin (906O0YJ6ZP) ; RNA, Ribosomal, 16S ; storax ; Methane (OP0UW79H66)
Language	English
Publishing date	2023-07-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1358023-1
ISSN	1365-2672 ; 1364-5072
ISSN (online)	1365-2672
ISSN	1364-5072
DOI	10.1093/jambio/lxad154
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Article: Winery by-products as a feed source with functional properties: dose-response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC.

Khiaosa-Ard, Ratchaneewan / Mahmood, Mubarik / Mickdam, Elsayed / Pacífico, Cátia / Meixner, Julia / Traintinger, Laura-Sophie

Journal of animal science and biotechnology

2023 Volume 14, Issue 1, Page(s) 92

Abstract: Background: Grape and winery by-products have nutritional values for cattle and also contain functional compounds like phenols, which not only bind to protein but can also directly affect microbiota and their function in the rumen. We characterized the ... ...

Abstract	Background: Grape and winery by-products have nutritional values for cattle and also contain functional compounds like phenols, which not only bind to protein but can also directly affect microbiota and their function in the rumen. We characterized the nutritional and functional effects of grape seed meal and grape pomace as well as an effective dosage of grape phenols on ruminal microbiota and fermentation characteristics using a rumen simulation technique. Results: Six diets (each n = 8) were compared including a control diet (CON, no by-product), a positive control diet (EXT, CON + 3.7% grape seed extract on a dry matter (DM) basis), two diets with grape seed meal at 5% (GS-low) and 10% (GS-high), and two diets with grape pomace: at 10% (GP-low) and 20% (GP-high), on a DM basis. The inclusion of the by-product supplied total phenols at 3.4%, 0.7%, 1.4%, 1.3%, and 2.7% of diet DM for EXT, GS-low, GS-high, GP-low, and GP-high, respectively. Diets were tested in four experimental runs. All treatments decreased ammonia concentrations and the disappearances of DM and OM (P < 0.05) compared to CON. EXT and GP-high lowered butyrate and odd- and branch-chain short-chain fatty acids while increased acetate compared to CON (P < 0.05). Treatments did not affect methane formation. EXT decreased the abundance of many bacterial genera including those belonging to the core microbiota. GP-high and EXT consistently decreased Olsenella and Anaerotipes while increased Ruminobacter abundances. Conclusion: The data suggest that the inclusion of winery by-products or grape seed extract could be an option for reducing excessive ammonia production. Exposure to grape phenols at a high dosage in an extract form can alter the rumen microbial community. This, however, does not necessarily alter the effect of grape phenols on the microbial community function compared to feeding high levels of winery by-products. This suggests the dominant role of dosage over the form or source of the grape phenols in affecting ruminal microbial activity. In conclusion, supplementing grape phenols at about 3% of diet DM is an effective dosage tolerable to ruminal microbiota.
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2630162-3
ISSN	2049-1891 ; 1674-9782
ISSN (online)	2049-1891
ISSN	1674-9782
DOI	10.1186/s40104-023-00892-7
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Article ; Online: Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves.

Hartinger, Thomas / Pacífico, Cátia / Sener-Aydemir, Arife / Poier, Gregor / Kreuzer-Redmer, Susanne / Terler, Georg / Klevenhusen, Fenja / Zebeli, Qendrim

Animal microbiome

2024 Volume 6, Issue 1, Page(s) 12

Abstract: Background: Recent data indicated similar growth performance of young calves fed solely high-quality hay instead of a starter diet based on starchy ingredients. Yet, providing exclusively such distinct carbohydrate sources during early life might ... ...

Abstract	Background: Recent data indicated similar growth performance of young calves fed solely high-quality hay instead of a starter diet based on starchy ingredients. Yet, providing exclusively such distinct carbohydrate sources during early life might specifically prime the microbiota and gene expression along the gut of young calves, which remains to be explored. We investigated the effects of starter diets differing in carbohydrate composition, that is medium- or high-quality hay and without or with 70% concentrate supplementation (on fresh matter basis), across the gastrointestinal tract (GIT) of weaned Holstein calves (100 ± 4 days of age) using 16 S rRNA gene sequencing and analyses of short-chain fatty acids and host epithelial gene expressions. Results: The concentrate supplementation drastically decreased microbial diversity throughout the gut, which was also true to a much lesser extent for high-quality hay when compared to medium-quality hay in the foregut. Similarly, the factor concentrate strongly shaped the diet-associated common core microbiota, which was substantially more uniform along the gut with concentrate supplementation. The fermentation profile shifted towards less acetate but more propionate with concentrate supplementation in almost all gut sections, corresponding with higher abundances of starch-utilizing bacteria, while major fibrolytic clusters declined. Noteworthy, the n-butyrate proportion decreased in the rumen and increased in the colon with concentrate, showing an opposite, gut site-dependent effect. Both dietary factors modestly influenced the host epithelial gene expression. Conclusions: Concentrate supplementation clearly primed the microbial ecosystem on a starch-targeted fermentation with characteristic genera occupying this niche along the entire GIT of calves, whereas the microbial differentiation due to hay quality was less distinct. Overall, changes in the microbial ecosystem were only marginally reflected in the targeted transcriptional profile of the host epithelium.
Language	English
Publishing date	2024-03-13
Publishing country	England
Document type	Journal Article
ISSN	2524-4671
ISSN (online)	2524-4671
DOI	10.1186/s42523-024-00297-5
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Article: Short-term exposure to the mycotoxins zearalenone or fumonisins affects rumen fermentation and microbiota, and health variables in cattle

Hartinger, Thomas / Grabher, Lena / Pacífico, Cátia / Angelmayr, Barbara / Faas, Johannes / Zebeli, Qendrim

Food and chemical toxicology. 2022 Apr., v. 162

2022

Abstract: Zearalenone (ZEN) and fumonisins (FUM) jeopardize fertility and health in cattle; yet, their toxigenic effects on rumen health and microbiota, both being crucial for animal health, are not clarified. This study determined the effects of a short-term ... ...

Abstract	Zearalenone (ZEN) and fumonisins (FUM) jeopardize fertility and health in cattle; yet, their toxigenic effects on rumen health and microbiota, both being crucial for animal health, are not clarified. This study determined the effects of a short-term exposure to ZEN or FUM on the rumen ecosystem, and further evaluated acute implications on health parameters. Six cows were fed a basal diet with 40% grain (dry matter basis) and exposed to either 5 mg of ZEN or 20 mg of FUM daily for two consecutive days each, separated by a 7-days washout period. The exposure to ZEN or FUM led to a reduction of Lachnospiraceae and Prevotellaceae in the rumen. Similarly, ZEN lowered the ruminal pH and total short-chain fatty acid concentration, despite increased rumination activity of the cows. Fumonisins increased the number of observed features and significantly impacted β-diversity structure and metagenome predicted function. At the systemic level, FUM exposure suggested an immediate hepatotoxic effect, as evidenced by increased liver enzyme concentrations, which were accompanied by altered heart and respiratory rates. Similarly, ZEN increased the body temperature up to a mild fever. Concluding, short-term exposure to ZEN and FUM can harm the rumen ecosystem and acutely impair systemic health.
Keywords	Lachnospiraceae ; acute exposure ; animal health ; diet ; ecosystems ; enzymes ; fatty acid composition ; fermentation ; fever ; fumonisins ; heart ; hepatotoxicity ; liver ; metagenomics ; microorganisms ; pH ; rumination ; short chain fatty acids ; toxicology ; zearalenone
Language	English
Dates of publication	2022-04
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	782617-5
ISSN	1873-6351 ; 0278-6915
ISSN (online)	1873-6351
ISSN	0278-6915
DOI	10.1016/j.fct.2022.112900
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Article ; Online: Shift of dietary carbohydrate source from milk to various solid feeds reshapes the rumen and fecal microbiome in calves.

Hartinger, Thomas / Pacífico, Cátia / Poier, Gregor / Terler, Georg / Klevenhusen, Fenja / Zebeli, Qendrim

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12383

Abstract: The transition from milk to solid diets drastically impacts the gut microbiome of calves. We explored the microbial communities of ruminal fluid and feces of Holstein calves when fed milk on d 7 of life, and when fed solid feeds based on either medium- ... ...

Abstract	The transition from milk to solid diets drastically impacts the gut microbiome of calves. We explored the microbial communities of ruminal fluid and feces of Holstein calves when fed milk on d 7 of life, and when fed solid feeds based on either medium- or high-quality hay with or without concentrate inclusion (70% in fresh matter) on d 91. Ruminal fluid and feces had distinct microbial compositions already on d 7, showing that niche specialization in early-life gut is rather diet-independent. Changes between d 7 and d 91 were accompanied by a general increase in microbial diversity. Solid diets differed largely in their carbohydrate composition, being reflected in major changes on d 91, whereby concentrate inclusion was the main driver for differences among groups and strongly decreased microbial diversity in both matrices. Fecal enterotyping revealed two clusters: concentrate-supplemented animals had an enterotype prevalent in Prevotella, Succinivibrio and Anaerovibrio, whereas the enterotype of animals without concentrate was dominated by fibrolytic Ruminococcaceae. Hay quality also affected microbial composition and, compared to medium-quality, high-quality hay reduced alpha-diversity metrics. Concluding, our study revealed that concentrate inclusion, more than hay quality, dictates the establishment of niche-specific, microbial communities in the rumen and feces of calves.
MeSH term(s)	Animal Feed/analysis ; Animals ; Cattle ; Diet/veterinary ; Dietary Carbohydrates/metabolism ; Feces ; Fermentation ; Microbiota ; Milk ; Rumen/metabolism
Chemical Substances	Dietary Carbohydrates
Language	English
Publishing date	2022-07-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16052-2
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Article ; Online: Short-term exposure to the mycotoxins zearalenone or fumonisins affects rumen fermentation and microbiota, and health variables in cattle.

Hartinger, Thomas / Grabher, Lena / Pacífico, Cátia / Angelmayr, Barbara / Faas, Johannes / Zebeli, Qendrim

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association

2022 Volume 162, Page(s) 112900

Abstract	Zearalenone (ZEN) and fumonisins (FUM) jeopardize fertility and health in cattle; yet, their toxigenic effects on rumen health and microbiota, both being crucial for animal health, are not clarified. This study determined the effects of a short-term exposure to ZEN or FUM on the rumen ecosystem, and further evaluated acute implications on health parameters. Six cows were fed a basal diet with 40% grain (dry matter basis) and exposed to either 5 mg of ZEN or 20 mg of FUM daily for two consecutive days each, separated by a 7-days washout period. The exposure to ZEN or FUM led to a reduction of Lachnospiraceae and Prevotellaceae in the rumen. Similarly, ZEN lowered the ruminal pH and total short-chain fatty acid concentration, despite increased rumination activity of the cows. Fumonisins increased the number of observed features and significantly impacted β-diversity structure and metagenome predicted function. At the systemic level, FUM exposure suggested an immediate hepatotoxic effect, as evidenced by increased liver enzyme concentrations, which were accompanied by altered heart and respiratory rates. Similarly, ZEN increased the body temperature up to a mild fever. Concluding, short-term exposure to ZEN and FUM can harm the rumen ecosystem and acutely impair systemic health.
Language	English
Publishing date	2022-03-02
Publishing country	England
Document type	Journal Article
ZDB-ID	782617-5
ISSN	1873-6351 ; 0278-6915
ISSN (online)	1873-6351
ISSN	0278-6915
DOI	10.1016/j.fct.2022.112900
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Article: Characterization of microbial intolerances and ruminal dysbiosis towards different dietary carbohydrate sources using an in vitro model

Kheirandish, Parisa / Petri, Renee Maxine / Sener‐Aydemir, Arife / Schwartz‐Zimmermann, Heidi Elisabeth / Berthiller, Franz / Zebeli, Qendrim / Pacífico, Cátia

Journal of applied microbiology. 2022 Aug., v. 133, no. 2

2022

Abstract: AIM: This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis. METHODS AND RESULTS: A metabologenomics approach was used to characterize dynamic microbial and ...

Abstract	AIM: This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis. METHODS AND RESULTS: A metabologenomics approach was used to characterize dynamic microbial and metabolomics shifts using the rumen simulation technique (RUSITEC) by feeding native cornstarch (ST), chemically modified cornstarch (CMS), or sucrose (SU). SU and CMS elicited the most drastic changes as rapidly as 4 h after feeding. This was accompanied by a swift accumulation of d‐lactate, and the decline of benzoic and malonic acid. A consistent increase in Bifidobacterium and Lactobacillus as well as a decrease in fibrolytic bacteria was observed for both CMS and ST after 24 h, indicating intolerances within the fibre degrading populations. However, an increase in Lactobacillus was already evident in SU after 8 h. An inverse relationship between Fibrobacter and Bifidobacterium was observed in ST. In fact, Fibrobacter was positively correlated with several short‐chain fatty acids, while Lactobacillus was positively correlated with lactic acid, hexoses, hexose‐phosphates, pentose phosphate pathway (PENTOSE‐P‐PWY), and heterolactic fermentation (P122‐PWY). CONCLUSIONS: The feeding of sucrose and modified starches, followed by native cornstarch, had a strong disruptive effect in the ruminal microbial community. Feed intolerances were shown to develop at different rates based on the availability of glucose for ruminal microorganisms. SIGNIFICANCE AND IMPACT OF THE STUDY: These results can be used to establish patterns of early dysbiosis (biomarkers) and develop strategies for preventing undesirable shifts in the ruminal microbial ecosystem.
Keywords	Bifidobacterium ; Fibrobacter ; Lactobacillus ; biomarkers ; corn starch ; dietary carbohydrate ; dysbiosis ; fermentation ; glucose ; hexoses ; lactic acid ; malonic acid ; metabolomics ; microbial communities ; models ; pentose phosphate cycle ; ruminal acidosis ; sucrose
Language	English
Dates of publication	2022-08
Size	p. 458-476.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1358023-1
ISSN	1365-2672 ; 1364-5072
ISSN (online)	1365-2672
ISSN	1364-5072
DOI	10.1111/jam.15573
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Article ; Online: Characterization of microbial intolerances and ruminal dysbiosis towards different dietary carbohydrate sources using an in vitro model.

Kheirandish, Parisa / Petri, Renee Maxine / Sener-Aydemir, Arife / Schwartz-Zimmermann, Heidi Elisabeth / Berthiller, Franz / Zebeli, Qendrim / Pacífico, Cátia

Journal of applied microbiology

2022 Volume 133, Issue 2, Page(s) 458–476

Abstract: Aim: This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis.: Methods and results: A metabologenomics approach was used to characterize dynamic ... ...

Abstract	Aim: This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis. Methods and results: A metabologenomics approach was used to characterize dynamic microbial and metabolomics shifts using the rumen simulation technique (RUSITEC) by feeding native cornstarch (ST), chemically modified cornstarch (CMS), or sucrose (SU). SU and CMS elicited the most drastic changes as rapidly as 4 h after feeding. This was accompanied by a swift accumulation of d-lactate, and the decline of benzoic and malonic acid. A consistent increase in Bifidobacterium and Lactobacillus as well as a decrease in fibrolytic bacteria was observed for both CMS and ST after 24 h, indicating intolerances within the fibre degrading populations. However, an increase in Lactobacillus was already evident in SU after 8 h. An inverse relationship between Fibrobacter and Bifidobacterium was observed in ST. In fact, Fibrobacter was positively correlated with several short-chain fatty acids, while Lactobacillus was positively correlated with lactic acid, hexoses, hexose-phosphates, pentose phosphate pathway (PENTOSE-P-PWY), and heterolactic fermentation (P122-PWY). Conclusions: The feeding of sucrose and modified starches, followed by native cornstarch, had a strong disruptive effect in the ruminal microbial community. Feed intolerances were shown to develop at different rates based on the availability of glucose for ruminal microorganisms. Significance and impact of the study: These results can be used to establish patterns of early dysbiosis (biomarkers) and develop strategies for preventing undesirable shifts in the ruminal microbial ecosystem.
MeSH term(s)	Animal Feed/analysis ; Animals ; Diet ; Dietary Carbohydrates/analysis ; Dietary Carbohydrates/metabolism ; Dysbiosis/metabolism ; Dysbiosis/veterinary ; Fermentation ; Fibrobacter ; Lactobacillus/metabolism ; Microbiota ; Rumen/microbiology ; Starch/metabolism ; Sucrose/metabolism
Chemical Substances	Dietary Carbohydrates ; Sucrose (57-50-1) ; Starch (9005-25-8)
Language	English
Publishing date	2022-04-18
Publishing country	England
Document type	Journal Article
ZDB-ID	1358023-1
ISSN	1365-2672 ; 1364-5072
ISSN (online)	1365-2672
ISSN	1364-5072
DOI	10.1111/jam.15573
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Article ; Online: Draft Genome Sequence of Escherichia coli DSM 12242, a Highly Efficient Host Strain for the Isolation of Somatic Coliphages.

Pacífico, Cátia / Sofka, Dmitrij / Carriço, João André / Hilbert, Friederike

Microbiology resource announcements

2019 Volume 8, Issue 38

Abstract: Here, we report the draft genome sequence and characterization of the commercial ... ...

Abstract	Here, we report the draft genome sequence and characterization of the commercial strain
Language	English
Publishing date	2019-09-19
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00953-19
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