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Animals
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The Animal Microbiome in Health and Disease
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The Animal Microbiome in Health and Disease

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Nutrition".

Deadline for manuscript submissions: 1 August 2024 | Viewed by 8943

Special Issue Editor

Dr. Kelsy J. Robinson

E-Mail Website
Guest Editor
Poultry Production and Product Safety Research Unit, USDA–Agricultural Research Service (ARS), Fayetteville, AR, USA
Interests: gut health; microbiome; poultry; immunology; host-pathogen interactions

Special Issue Information

Dear Colleagues,

Extensive work in recent years has significantly advanced our understanding of the integral role animal microbiomes play in maintaining health and productivity. Elegant research has demonstrated the association of microbial dysbiosis with disease states, the essential nature of commensal microbes for proper immune development, the crosstalk between microorganisms and their hosts, and much more. However, additional work is needed to fully comprehend the microbiomes of various niches within the body and the ways in which they influence, and are influenced by, their hosts.  

In this Special Issue, we invite original research articles and review papers. Research projects may include, but are not limited to, the association between microbiome composition or function and disease, stress, or production parameters. Additional topics may include the characterization of smaller microbial populations (i.e., fungi, viruses, protozoa), the gut–brain axis, and the association between microbial metabolites and the host.

I look forward to receiving your contributions.

Dr. Kelsy J. Robinson
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiome
  • mycobiome
  • gut–brain axis
  • gut health
  • metagenomics
  • metabolomics
  • transcriptomics
  • host–pathogen interaction
  • livestock
  • poultry

Published Papers (7 papers)

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Research

21 pages, 2950 KiB  
Article
Role of Maternal Antibodies in the Protection of Broiler Chicks against Campylobacter Colonization in the First Weeks of Life
by Kristof Haems, Diederik Strubbe, Nathalie Van Rysselberghe, Geertrui Rasschaert, An Martel, Frank Pasmans and An Garmyn
Animals 2024, 14(9), 1291; https://doi.org/10.3390/ani14091291 - 25 Apr 2024
Abstract
Thermophilic Campylobacter species are the most common cause of bacterium-mediated diarrheal disease in humans globally. Poultry is considered the most important reservoir of human campylobacteriosis, but so far, no effective countermeasures are in place to prevent the bacterium from colonizing broiler flocks. This [...] Read more.
Thermophilic Campylobacter species are the most common cause of bacterium-mediated diarrheal disease in humans globally. Poultry is considered the most important reservoir of human campylobacteriosis, but so far, no effective countermeasures are in place to prevent the bacterium from colonizing broiler flocks. This study investigated maternal antibodies’ potential to offer protection against Campylobacter in broiler chicks via a field trial and an immunization trial. In the field trial, breeder flocks with high and low anti-Campylobacter antibody levels in the yolk were selected based on serological screening. Offspring were subsequently monitored for maternal antibodies and Campylobacter prevalence during early life. Although maternal antibodies declined rapidly in the serum of broilers, offspring from flocks with lower anti-Campylobacter antibody levels seemed to be more susceptible to colonization. In the immunization trial, breeders from a seropositive breeder flock were vaccinated with an experimental bacterin or subunit vaccine. Immunization increased antibody levels in the yolk and consequently in the offspring. Elevated maternal antibody levels were significantly associated with reduced Campylobacter susceptibility in broilers at 2 weeks old but not at 1 and 3 weeks old. Overall, the protective effect of maternal immunity should be cautiously considered in the context of Campylobacter control in broilers. Immunization of breeders may enhance resistance but is not a comprehensive solution. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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13 pages, 2113 KiB  
Article
Exploring Bile-Acid Changes and Microflora Profiles in Chicken Fatty Liver Disease Model
by Wen-Yuan Yang, Pei-En Chang, Sin-Jin Li, Shih-Torng Ding and Yuan-Yu Lin
Animals 2024, 14(7), 992; https://doi.org/10.3390/ani14070992 - 23 Mar 2024
Viewed by 596
Abstract
Excessive liver fat causes non-alcoholic fatty liver disease (NAFLD) in laying hens, reducing egg production. Addressing NAFLD via bile-acid metabolism is gaining attention. We induced NAFLD in 7-week-old ISA female chickens with a high-cholesterol, low-choline diet (CLC) for 6 weeks. LC/MS was used [...] Read more.
Excessive liver fat causes non-alcoholic fatty liver disease (NAFLD) in laying hens, reducing egg production. Addressing NAFLD via bile-acid metabolism is gaining attention. We induced NAFLD in 7-week-old ISA female chickens with a high-cholesterol, low-choline diet (CLC) for 6 weeks. LC/MS was used to analyze serum and cecal bile acids, while cecal digesta DNA underwent 16S rRNA sequencing. The distribution of bile acid varied in healthy (CON) and CLC-fed chickens. CLC increased secondary bile acids (TLCA, TUDCA, THDCA, TDCA) in serum and primary bile acids (CDCA, TCDCA, isoDCA) in serum, as well as glycochenodeoxycholic acid (GCDCA) in cecal contents. CLC upregulated bile-acid synthesis enzymes (CYP7A1, CYP8B1) in the liver. Bile-acid receptor gene expression (HNF4A, FXR, LXR) was similar between groups. Microbiota abundance was richer in CON (alpha-diversity), with distinct separation (beta-diversity) between CON and CLC. The Firmicutes/Bacteroidetes ratio slightly decreased in CLC. Taxonomic analysis revealed higher Bacteroides, Alistipes, Megamonas in CLC but lower Barnesiella. CLC had more Mucispirillum, Eubacterium_coprostanoligenes_group, Shuttleworthia, and Olsenella, while CON had more Enterococcus, Ruminococcaceae_UCG_014, and Faecalibacterium. This study unveils bile-acid and microflora changes in a chicken NAFLD model, enhancing our understanding of fatty liver disease metabolism and aiding targeted interventions. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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19 pages, 11958 KiB  
Article
Gut Microbial Diversity Analysis of Different Native Chickens and Screening of Chicken-Derived Probiotics
by Lu Chen, Xue Bai, Tao Wang, Jia Liu, Xiaomeng Miao, Bo Zeng and Diyan Li
Animals 2023, 13(23), 3672; https://doi.org/10.3390/ani13233672 - 27 Nov 2023
Viewed by 928
Abstract
The gut microbiota plays a critical role in the growth, development, nutritional digestion, and overall health of chickens. Furthermore, certain probiotics isolated from poultry intestines have demonstrated the potential to enhance immune function and production performance in chickens. To investigate the differences in [...] Read more.
The gut microbiota plays a critical role in the growth, development, nutritional digestion, and overall health of chickens. Furthermore, certain probiotics isolated from poultry intestines have demonstrated the potential to enhance immune function and production performance in chickens. To investigate the differences in gut microbiota among chickens from various geographical environments and different breeds of broiler and laying hens, we conducted 16S rRNA sequencing on the fecal microbiota of 140 Chinese native chickens and ten Roman layers. In addition, we isolated and screened the potential probiotics to examine their biological characteristics, genome profiles, and functionality in animals. Our findings revealed the significant variations in gut microbiota composition and structure between Tibetan chickens (ZJ), which reside in high-altitude regions, and Meihua chickens (MH) and Xuhai chickens (XH), which inhabit low-altitude regions. Specifically, Cupriavidus and Candidatus_Bacilloplasma were identified as unique microbial communities in high and low altitudes, respectively. Notably, among regions with similar altitudes, Luning chickens (LN) exhibited the lowest α diversity, accompanied by a remarkably high relative abundance of Firmicutes and Lactobacillus. Conversely, Wugu chickens (WGs) and Yaoshan chickens (YSs) displayed similar gut microbiota profiles. Furthermore, distinctive gut microbiota patterns were observed between the different breeds of broilers and laying hens. Commercial Roman layers (LMs) exhibited significantly lower alpha diversity compared to native chickens, and broilers and laying hens predominantly harbored Firmicutes, Bacteroidota, and Proteobacteria. Of particular interest, the probiotics Lactobacillus agilis MH1 and Lactobacillus salivarius ZJ1, derived from chicken feces, exhibited favorable genomic profiles, and demonstrated anti-colitis effects and immunomodulatory functions. These findings provide a crucial theoretical foundation for native chicken research and offer insights for the future development and formulation of chicken-derived probiotics. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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22 pages, 2440 KiB  
Article
Temporal Microbial Dynamics in Feces Discriminate by Nutrition, Fecal Color, Consistency and Sample Type in Suckling and Newly Weaned Piglets
by Barbara U. Metzler-Zebeli, Frederike Lerch, Fitra Yosi, Julia Vötterl, Juliane Ehmig, Simone Koger and Doris Verhovsek
Animals 2023, 13(14), 2251; https://doi.org/10.3390/ani13142251 - 09 Jul 2023
Viewed by 1136
Abstract
Feces enable frequent samplings for the same animal, which is valuable in studies investigating the development of the gut microbiome in piglets. Creep feed should prepare the piglet’s gut for the postweaning period and shape the microbiome accordingly. Little is known about the [...] Read more.
Feces enable frequent samplings for the same animal, which is valuable in studies investigating the development of the gut microbiome in piglets. Creep feed should prepare the piglet’s gut for the postweaning period and shape the microbiome accordingly. Little is known about the variation that is caused by differences in fecal color and consistency and different sample types (feces versus swab samples). Therefore, this study evaluated the age-related alterations in the microbiome composition (16S rRNA gene) in feces of suckling and newly weaned piglets in the context of nutrition and fecal consistency, color and sample type from day 2 to 34 of life. Feces from 40 healthy piglets (2 each from 20 litters) were collected on days 2, 6, 13, 20, 27, 30 and 34. Weaning occurred on day 28. Half of the litters only drank sow milk during the suckling phase, whereas the other half had access to creep feed from day 10. Creep feeding during the suckling phase influenced the age-related total bacterial and archaeal abundances but had less of an influence on the relative bacterial composition. Results further showed different taxonomic compositions in feces of different consistency, color and sample type, emphasizing the need to consider these characteristics in comprehensive microbiome studies. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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12 pages, 4225 KiB  
Article
Anaerobutyricum and Subdoligranulum Are Differentially Enriched in Broilers with Disparate Weight Gains
by Jing Liu, Kelsy Robinson, Wentao Lyu, Qing Yang, Jing Wang, Karen D. Christensen and Guolong Zhang
Animals 2023, 13(11), 1834; https://doi.org/10.3390/ani13111834 - 01 Jun 2023
Cited by 2 | Viewed by 1451
Abstract
The intestinal microbiota is critically important for animal health and productivity. However, the influence of the intestinal microbiota on animal growth efficiency remains elusive. This current study was aimed at identifying the intestinal bacteria that are associated with the growth rate of broilers [...] Read more.
The intestinal microbiota is critically important for animal health and productivity. However, the influence of the intestinal microbiota on animal growth efficiency remains elusive. This current study was aimed at identifying the intestinal bacteria that are associated with the growth rate of broilers in a commercial production setting. Ross 708 broilers with extremely high, medium, and extremely low body weight (BW) were separately selected for each sex from a house of approximately 18,000 chickens on day 42. The cecal content of each animal was subjected to 16S rRNA gene sequencing for microbiota profiling. Our results indicate that a number of bacteria were differentially enriched among different groups of broilers, with several showing a significant correlation (p < 0.05) with BW in both sexes or in a sex-specific manner. Subdoligranulum was drastically diminished in high-BW birds with a strong negative correlation with BW in both males and females. While one Anaerobutyricum strain showed a positive correlation with BW in both sexes, another strain of Anaerobutyricum was positively correlated with BW only in females. These sex-dependent and -independent bacteria could be targeted for improving the growth efficiency and may also be explored as potential biomarkers for the growth rate of broiler chickens. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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15 pages, 2699 KiB  
Article
Effect of Salmonella Typhimurium Colonization on Microbiota Maturation and Blood Leukocyte Populations in Broiler Chickens
by Kelsy Robinson, Anna L. F. V. Assumpcao, Komala Arsi, Gisela F. Erf, Annie Donoghue and Palmy R. R. Jesudhasan
Animals 2022, 12(20), 2867; https://doi.org/10.3390/ani12202867 - 20 Oct 2022
Cited by 4 | Viewed by 1841
Abstract
Reducing Salmonella in commercial chickens is vital to decreasing human salmonellosis infections resulting from contact with contaminated poultry and poultry products. As the intestinal microbiota plays an important role in preventing pathogen colonization, we sought to understand the relationship between Salmonella infection and [...] Read more.
Reducing Salmonella in commercial chickens is vital to decreasing human salmonellosis infections resulting from contact with contaminated poultry and poultry products. As the intestinal microbiota plays an important role in preventing pathogen colonization, we sought to understand the relationship between Salmonella infection and the cecal microbiota and the host immune system. Day-of-hatch broiler chicks were assigned to three treatments: control, artificial (SA), and natural (SN) Salmonella infection. At seven days of age, control and SA birds were inoculated with PBS or Salmonella Typhimurium, respectively. Five SA birds were transferred to SN cages to facilitate natural infection. Cecal content and blood samples were collected at 0, 8, 14, and 21 days of age for microbiota and leukocyte analysis, respectively. A significant change in microbiota composition was observed in both groups as noted by a decrease in Lactobacillus and Escherichia and an increase in Bacteroides. Leukocyte analysis revealed a decrease in the percentage of circulating monocytes at 7 days post-infection while a decrease in thrombocyte and an increase in heterophil percentages were seen at 14 days post-infection. Taken together, these results demonstrate the ability of Salmonella to modulate the intestinal microbiota to facilitate colonization. Additionally, results indicated an early role of monocytes and thrombocytes during colonization, followed by heterophils. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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11 pages, 1538 KiB  
Article
Insight into the Fecal Microbiota Signature Associated with Growth Specificity in Korean Jindo Dogs Using 16S rRNA Sequencing
by So-Young Choi, Bong-Hwan Choi, Ji-Hye Cha, Yeong-Jo Lim, Sunirmal Sheet, Min-Ji Song, Min-Jeong Ko, Na-Yeon Kim, Jong-Seok Kim, Seung-Jin Lee, Seok-Il Oh and Won-Cheoul Park
Animals 2022, 12(19), 2499; https://doi.org/10.3390/ani12192499 - 20 Sep 2022
Cited by 1 | Viewed by 1657
Abstract
Gut microbiomes are well recognized to serve a variety of roles in health and disease, even though their functions are not yet completely understood. Previous studies have demonstrated that the microbiomes of juvenile and adult dogs have significantly different compositions and characteristics. However, [...] Read more.
Gut microbiomes are well recognized to serve a variety of roles in health and disease, even though their functions are not yet completely understood. Previous studies have demonstrated that the microbiomes of juvenile and adult dogs have significantly different compositions and characteristics. However, there is still a scarcity of basic microbiome research in dogs. In this study, we aimed to advance our understanding by confirming the difference in fecal microbiome between young and adult dogs by analyzing the feces of 4-month and 16-month-old Jindo dogs, a domestic Korean breed. Microbiome data were generated and examined for the two age groups using 16S rRNA analysis. Comparison results revealed that the 16-month-old group presented a relatively high distribution of Bacteroides, whereas the 4-month-old group presented a comparatively high distribution of the Lactobacillus genus. Microbial function prediction analyses confirmed the relative abundance of lipid metabolism in 4-month-old dogs. In 16-month-old dogs, glucose metabolism was determined using microbial function prediction analyses. This implies that the functional microbiome changes similarly to the latter in adults compared with childhood. Overall, we discovered compositional and functional variations between genes of the gut microbial population in juveniles and adults. These microbial community profiles can be used as references for future research on the microbiome associated with health and development in the canine population. Full article
(This article belongs to the Special Issue The Animal Microbiome in Health and Disease)
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