Molecular ecological analysis of the gastrointestinal microbiota: a review

Sympathetic-Mediated Intestinal Cell Death Contributes to Gut Barrier Impairment After Stroke

Tissue injury induced by stroke is traditionally thought to be localised to the brain. However, there is an accumulating body of evidence to demonstrate that stroke promotes pathophysiological consequences in peripheral tissues including the gastrointestinal system. In this study, we investigated the mechanisms underlying gut permeability after stroke. We utilised the clinically relevant experimental model of stroke called permanent intraluminal middle cerebral artery occlusion (pMCAO) to examine the effect of cerebral ischaemia on the gut. We detected stroke-induced gut permeability at 5 h after pMCAO. At this timepoint, we observed significantly elevated intestinal epithelial cell death in post-stroke mice compared to their sham-operated counterparts. At 24 h after stroke onset when the gut barrier integrity is restored, our findings indicated that post-stroke intestinal epithelium had higher expression of genes associated with fructose metabolism, and hyperplasia of intestinal crypts and goblet cells, conceivably as a host compensatory mechanism to adapt to the impaired gut barrier. Furthermore, we discovered that stroke-induced gut permeability was mediated by the activation of the sympathetic nervous system as pharmacological denervation decreased the stroke-induced intestinal epithelial cell death, goblet cell and crypt hyperplasia, and gut permeability to baseline levels. Our study identifies a previously unknown mechanism in the brain-gut axis by which stroke triggers intestinal cell death and gut permeability.

Effects of organic acid-preserved cereal grains in sow diets during late gestation and lactation on the performance and faecal microbiota of sows and their offspring

BACKGROUND

Organic acids (OA) and maternal nutritional strategies have been demonstrated to promote piglet health and development. The objective of this study was to investigate the effects of incorporating OA-preserved cereal grains into sow diets during late gestation and lactation, aiming to reduce the metabolic demands of lactation while optimising offspring development and growth until slaughter. The experiment compared OA-preserved wheat and barley to conventionally dried grains, focusing on sow and offspring performance, as well as their faecal microbiota during lactation. Forty sows were blocked based on parity, body weight and back fat thickness on d 100 of gestation and assigned to one of two diets: a dried grain lactation diet and a preserved grain lactation diet. Sow faecal samples were collected at farrowing for the coefficient of apparent total tract digestibility (CATTD) of nutrients and microbial analysis. Offspring faecal samples were collected on d 10 postpartum and at weaning (d 26 postpartum) for microbial analysis.

RESULTS

Sow body weight, back fat changes, gestation and lactation length, total piglets born, wean-to-oestrus interval, and lactation efficiency were unaffected by sow diet (P > 0.05). However, sows offered the preserved grain diet exhibited improved CATTD of dry matter, nitrogen, gross energy, and neutral detergent fibre (P < 0.05). While no maternal effect was observed on offspring growth during lactation (P > 0.05), pigs from sows offered the preserved grain diet showed improved growth and feed efficiency from weaning until slaughter (d 168) compared to those from sows offered the dried grain diet (P < 0.05). The preserved grain diet also reduced the abundance of Proteobacteria in sow faeces at farrowing and in their offspring on d 10 postpartum, and improved piglet faecal scores throughout lactation (P = 0.05). At weaning, piglets from sows offered the preserved grain diet exhibited an increased abundance of Lactobacillus and reduced abundance of Alistipes in their faeces (P < 0.05).

CONCLUSION

OA-preserved grains enhanced the CATTD of nutrients in sows, promoted healthier piglet faecal scores during lactation, and improved offspring growth performance post-weaning, potentially linked to beneficial changes observed in the faecal microbiota of sows and their offspring during lactation.

Effects of maternal-offspring supplementation of probiotics and synbiotics on the immunity of offspring Bama mini-pigs

Maternal nutrition is one of the main factors regulating the growth and immunity of piglets. This study aimed to investigate the effects of maternal or maternal-offspring supplementation of antibiotics, probiotics, and synbiotics on the immunity of offspring (21, 65, and 125 day-old) in Bama mini-pigs. The results showed that adding antibiotics to maternal diets increased the plasma IFN-γ level of offspring piglets at 21 day-old. Compared with maternal supplementation, maternal-offspring supplementation of antibiotics decreased the IL-10 level in the spleen, probiotics decreased IL-2, IL-10, and TNF-α levels in the ileum, and synbiotics decreased IL-10 and IFN-γ levels in the ileum of offspring piglets. Moreover, maternal-offspring antibiotics supplementation increased the IL-1β level in the ileum, while probiotics supplementation increased the IL-1β level in the spleen of offspring piglets. Maternal antibiotics supplementation increased the TNF-α level in the ileum at 95 day-old compared with maternal probiotics and synbiotics supplementation. Maternal-offspring antibiotics supplementation increased the IL-1β level in the ileum compared with the probiotics supplementation, while synbiotics supplementation increased the IL-6 level in the ileum than the probiotics and antibiotics supplementation at 95 day-old. Moreover, maternal-offspring probiotics supplementation increased the IL-1β level in the spleen of offspring pigs, which was higher than the maternal probiotics supplementation. These findings suggest that the immune function of the offspring piglets varied depending on the specific approach used for probiotics and synbiotics supplementation.

Classifying compounds as prebiotics - scientific perspectives and recommendations

Microbiomes provide key contributions to health and potentially important therapeutic targets. Conceived nearly 30 years ago, the prebiotic concept posits that targeted modulation of host microbial communities through the provision of selectively utilized growth substrates provides an effective approach to improving health. Although the basic tenets of this concept remain the same, it is timely to address certain challenges pertaining to prebiotics, including establishing that prebiotic-induced microbiota modulation causes the health outcome, determining which members within a complex microbial community directly utilize specific substrates in vivo and when those microbial effects sufficiently satisfy selectivity requirements, and clarification of the scientific principles on which the term 'prebiotic' is predicated to inspire proper use. In this Expert Recommendation, we provide a framework for the classification of compounds as prebiotics. We discuss ecological principles by which substrates modulate microbiomes and methodologies useful for characterizing such changes. We then propose statistical approaches that can be used to establish causal links between selective effects on the microbiome and health effects on the host, which can help address existing challenges. We use this information to provide the minimum criteria needed to classify compounds as prebiotics. Furthermore, communications to consumers and regulatory approaches to prebiotics worldwide are discussed.

Effects of concentrate feeding sequence on VFA production, and cecal microbiota of Dezhou donkeys by metagenomic technology

Microorganisms residing in the cecum of donkeys are crucial for physiological processes, nutrient metabolism, and immune function. Feeding methods can affect the dynamic balance of animal gut microbiota, thereby affecting indicators such as volatile fatty acids. This study explores suitable feeding methods to promote actual production by changing the feeding order of concentrate. Fifteen Dezhou donkeys with similar age and weight profiles were randomly divided into three groups with the concentrate feeding sequence: fiber-to-concentrate (FC), concentrate-to-fiber (CF), and total mixed ration (TMR). The experiment spanned a duration of 82 days. The analyses conducted were primarily aimed at determining the effects of feeding on gut microbes, primarily using metagenomic sequencing techniques. The experimental findings revealed that the levels of valeric acid were notably higher in the CF and TMR groups compared to the FC group (p < 0.05). These results suggest that the feeding sequence exerts a certain impact on the microbial composition within the cecum of Dezhou donkeys. At the phylum level, the predominant microbiota consisted of Firmicutes and Bacteroidetes, with the CF group displaying a higher relative abundance of Firmicutes compared to both the FC and TMR groups. At the genus level, Prevotella, Bacteroides, and Fibrobacter were the dominant bacterial genera identified in cecum. The functional gene annotation analysis indicated a significantly lower abundance of lacZ (K01190), Por/nifJ (K03737), and ppdK (K01006) genes in CF group relative to the FC and TMR groups (p < 0.05), highlighting their roles in galactose metabolism and glycolysis, respectively. Moreover, the CF group exhibited a higher concentration of antibiotic resistance genes (tetO and tet44) in the gut microbiota compared to the TMR and FC groups (p < 0.05), underscoring the presence of numerous antibiotic resistance genes within the phyla Bacteroidetes, Firmicutes, and Proteobacteria. In conclusion, different precision feed sequences significantly impact the levels of volatile fatty acids in Dezhou fattening donkeys, modify the composition and functional genes of the cecal microbiota, and elucidate the microbial mechanisms influenced by the feeding sequence on the growth and metabolism. These insights are anticipated to provide a foundation for the rational design of precision feed sequences in practical agricultural settings.

Understanding the Effect of Compound Probiotics on the Health of Rabbits and Its Mechanisms Through Metagenomics

In this study, we investigated the effects of probiotics on growth performance, immunity, intestinal flora, and antioxidant capacity of rabbits. Three hundred New Zealand white rabbits were randomly divided into four groups. Groups A, B, C, and D were the lactobacillus group, compound probiotic group, control group, and antibiotic group, respectively. The results showed compared with the control group, the average weight of groups A, B, and D increased by 14.88%, 12.33%, and 11.97%, respectively. Moreover, the index of immune organs and the IgG and IgM in serum of group B were significantly increased (P < 0.05). Meanwhile, the activities of superoxide dismutase (SOD) in group B and catalase (CAT) in group A were significantly increased (P < 0.05). At week 5, the contents of rabbit cecum were taken for metagenome sequencing, and the results showed probiotics increased the relative abundance of Akkermansia, and decreased the relative abundance of Bacteroides. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found probiotics could enrich metabolic pathways such as carbohydrates, amino acids, and lipids. According to the Comprehensive Antibiotic Resistance Database (CARD), we found antibiotic resistance ontology (ARO) in cecum mainly included β-lactamases, macrolide 2'-phosphotransferase II, and plasmid-mediated quinolone resistance protein. Among them, there were 1964, 2105, and 1982 types of ARO in group B, group D, and groups A and C, respectively. These results showed probiotics played a beneficial role in maintaining or enhancing the health and growth of rabbits and could replace antibiotics under certain feeding conditions.

Gut microbiota composition in patients with Crohn's disease in Saudi Arabia

Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.

Microbiota-Accessible Boron-Containing Compounds in Complex Regional Pain Syndrome

The microbiota-gut-brain axis has garnered increasing attention in recent years for its role in various health conditions, including neuroinflammatory disorders like complex regional pain syndrome (CRPS). CRPS is a debilitating condition characterized by chronic neuropathic pain, and its etiology and pathophysiology remain elusive. Emerging research suggests that alterations in the gut microbiota composition and function could play a significant role in CRPS development and progression. Our paper explores the implications of microbiota in CRPS and the potential therapeutic role of boron (B). Studies have demonstrated that individuals with CRPS often exhibit dysbiosis, with imbalances in beneficial and pathogenic gut bacteria. Dysbiosis can lead to increased gut permeability and systemic inflammation, contributing to the chronic pain experienced in CRPS. B, an essential trace element, has shown promise in modulating the gut microbiome positively and exerting anti-inflammatory effects. Recent preclinical and clinical studies suggest that B supplementation may alleviate neuropathic pain and improve CRPS symptoms by restoring microbiota balance and reducing inflammation. Our review highlights the complex interplay between microbiota, inflammation, and neuropathic pain in CRPS and underscores the potential of B as a novel therapeutic approach to target the microbiota-gut-brain axis, offering hope for improved management of this challenging condition.

Basic constituents, bioactive compounds and health-promoting benefits of wine skin pomace: A comprehensive review

Wine pomace (WP) is a major byproduct generated during winemaking, and skin pomace (SKP) comprises one of the most valuable components of WP. Since SKP differs in composition and properties from seed pomace (SDP), precise knowledge of SKP will aid the wine industry in the development of novel, high-value products. The current review summarizes recent advances in research relating to SKP presents a comprehensive description of the generation, composition, and bioactive components, primarily focusing on the biological activities of SKP, including antioxidant, gastrointestinal health promotion, antibacterial, anti-inflammatory, anticancer, and metabolic disease alleviation properties. Currently, the separation and recovery of skins and seeds is an important trend in the wine industry for the disposal of winemaking byproducts. In comparison to SDP, SKP is rich in polyphenols including anthocyanins, flavonols, phenolic acids, stilbenes, and some proanthocyanidins, as well as dietary fiber (DF). These distinctive benefits afford SKP the opportunity for further development and application. Accordingly, the health-promoting mechanism and appropriate application of SKP will be further elucidated in terms of physiological activity, with the progress of biochemical technology and the deepening of related research.

The Naked Neck Gene in the Domestic Chicken: A Genetic Strategy to Mitigate the Impact of Heat Stress in Poultry Production—A Review

The poultry sector is one of the most important food industries in the world. Poultry production generates high-value protein products (meat and eggs) that are produced efficiently without the need for large areas. In poultry production, especially in the tropics, environmental factors, such as temperature and humidity, play a major role. Heat stress (HS) causes behavioral, physical, and physiological changes in poultry, with severe financial impacts. Therefore, it is important to find strategies to minimize it. The naked neck (Na) is an autosomal, incompletely dominant gene. Compared with normal feathered birds, these animals are known for their ability to adapt, perform, and reproduce under hot and humid climate conditions. Due to the absence of feathers on the neck, these animals increase heat dissipation, alleviating adverse heat effects, especially on productive performance. Genetic improvement of heat tolerance may provide a low-cost solution, of particular interest for developing countries in the tropics. The focus of this review is to evaluate the impact of HS in poultry with a special emphasis on the advantages of using the Na gene.

Comparison of enrichment methods for isolating Enterohemorrhagic Escherichia coli in kimchi

This study was conducted to compare the efficiency of four enrichment methods of Enterohemorrhagic Escherichia coli by using the 16S rRNA amplicon sequencing and a predictive model. Four different methods (US FDA, ISO, Japan Food Hygiene Association and Korea Ministry of Food and Drug Safety) were used to enrich EHEC in kimchi inoculated with cocktails of EHEC strains (NCCP 13720, NCCP 13721, and NCCP 14134). The maximum growth rate (μ_max) and lag phase duration (LPD) were compared using the Baranyi model, and 16S rRNA targeted sequencing was performed with samples at the end of the exponential phase. As a result, the μ_max and LPD values of Baranyi model developed for the four enriched media ranged from 0.82 to 0.92 and from 2.35 to 2.68, respectively, suggesting that the growth of EHEC was similar in all four enrichment media. As for the relative abundance of the bacterial composition at the family level, Enterobacteriaceae was identified as the major component (>50%) in all four enriched media. The relative abundance of Enterobacteriaceae was highest (>90%) in the two enriched media with 20 mg/L novobiocin, demonstrating that significant growth of non-targeted bacteria takes place in enrichment broths utilizing <20 mg/L novobiocin or different antibiotics. In conclusion, this study suggests that all four enrichment broth are suitable for growing EHEC in kimchi and the use and concentration of antibiotics such as novobiocin in enrichment media may have a critical role in species diversity.

Profile of the Gut Microbiome Containing Carbapenem-Resistant Enterobacteriaceae in ICU Patients

Carbapenem-resistant Enterobacteriaceae (CRE) is a risk to public health worldwide and causes epidemic outbreaks in hospitals. The identification of alterations in the gut microbial profile can potentially serve as an early diagnostic tool to prevent harmful bacterial colonization. The purpose of this study was to characterize the gut microbiota profile of CRE-positive stool samples using 16S rRNA gene sequencing and to compare it with that of healthy control groups at King AbdulAziz University Hospital. Our results demonstrate that compared to the control group samples, the CRE-positive and CRE-negative group samples were less diverse and were dominated by a few operational taxonomic clusters of Enterococcus, Sphingomonas, and Staphylococcus. An analysis of samples from CRE-positive patients revealed Pseudomonas as the most abundant taxon. The existence of Pseudomonas in clinical samples undoubtedly indicates the development of resistance to a variety of antimicrobial drugs, with a less diverse microbiota. In our study, we found that the co-occurrence patterns of Klebsiella, Parabacteroides, Proteus and Pseudomonas differed between the CRE-negative and control stool groups.

Unbalanced relationships: insights into the interaction between gut microbiota, geohelminths, and schistosomiasis

Hosts and their microbiota and parasites have co-evolved in an adaptative relationship since ancient times. The interaction between parasites and intestinal bacteria in terms of the hosts' health is currently a subject of great research interest. Therapeutic interventions can include manipulations of the structure of the intestinal microbiota, which have immunological interactions important for modulating the host's immune system and for reducing inflammation. Most helminths are intestinal parasites; the intestinal environment provides complex interactions with other microorganisms in which internal and external factors can influence the composition of the intestinal microbiota. Moreover, helminths and intestinal microorganisms can modulate the host's immune system either beneficially or harmfully. The immune response can be reduced due to co-infection, and bacteria from the intestinal microbiota can translocate to other organs. In this way, the treatment can be compromised, which, together with drug resistance by the parasites makes healing even more difficult. Thus, this work aimed to understand interactions between the microbiota and parasitic diseases caused by the most important geohelminths and schistosomiasis and the consequences of these associations.

Physico-Chemical and Metagenomic Profile Analyses of Animal Manures Routinely Used as Inocula in Anaerobic Digestion for Biogas Production

Anaerobic digestion (AD) of organic waste is considered a sustainable solution to energy shortage and waste management challenges. The process is facilitated by complex communities of micro-organisms, yet most wastes do not have these and thus need microbial inoculation using animal manures to initiate the process. However, the degradation efficiency and methane yield achieved in using different inocula vary due to their different microbial diversities. This study used metagenomics tools to compare the autochthonous microbial composition of cow, pig, chicken, and horse manures commonly used for biogas production. Cows exhibited the highest carbon utilisation (>30%) and showed a carbon to nitrogen ratio (C/N) favourable for microbial growth. Pigs showed the least nitrogen utilisation (<3%) which explains their low C/N whilst horses showed the highest nitrogen utilisation (>40%), which explains its high C/N above the optimal range of 20−30 for efficient AD. Manures from animals with similar gastrointestinal tract (GIT) physiologies were observed to largely harbour similar microbial communities. Conversely, some samples from animals with different GITs also shared common microbial communities plausibly because of similar diets and rearing conditions. Insights from this study will lay a foundation upon which in-depth studies of AD metabolic pathways and strategies to boost methane production through efficient catalysis can be derived.

Melatonin promotes the growth and development of lambs by increasing growth hormone and testosterone, targeting on apoptosis signaling pathway and intestinal microflora

Melatonin is an indole-like neuroendocrine hormone. A large number of studies have shown that melatonin can improve production performance of ewes, but it is not clear in lambs. In this study, the growth and development of the 2-month-old lambs implanted with melatonin were monitored for 60 days. The results showed that the growth rate of body weight and body skew length of lambs with melatonin treatment were significantly improved compared to the controls. The similar results were also observed in red blood cell count, hematocrit, red blood cell volume distribution width, the levels of growth hormone, testosterone, immunoglobulin A, immunoglobulin M and albumin. In addition, the cross sectional area of muscle fibers and adipose cells of lambs with melatonin implantation were also significantly increased compared to the controls (P<0.05). To further explore the potential mechanisms, the muscle and adipose tissue were selected for transcriptome sequencing. KEGG enrichment results showed that melatonin regulated the expression of genes related to apoptotic signaling pathway in muscle and adipocytes. Since the intestinal microbiota are involved in the nutritional balance and animal growth, the 16SrRNA sequencing related to the intestinal microbiota was also performed. The data indicated that the structural differences of fecal microflora mainly occur in the pathways of Cardiovascular disease, Excretory system and Signaling molecules and interaction. In brief, melatonin promotes the growth and development of lambs. The potential mechanisms may be that melatonin increased the growth hormone and testosterone mediated apoptosis signaling pathway and regulated intestinal microbial flora. Our results provide valuable information for melatonin to improve the production of sheep husbandry in the future.

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.

Nutrition and Digestive Physiology of the Broiler Chick: State of the Art and Outlook

Simple Summary

The first week after hatch is the most challenging period in the life of broilers. The digestive tract of the newly hatched chick is immature and must undergo dramatic changes before it can efficiently digest and absorb nutrients. The gut is the vital organ where nutrient digestion and absorption take place. Ontogenic changes that accompany improved digestion and absorption include increased secretion of digestive enzymes, increase in the gut absorptive surface area, and enhanced nutrient transporters. The obvious limiting factors are the secretion and activities of digestive enzymes, and the surface area for absorption. These limitations are overcome as the birds grow older, with concurrent improvements in nutrient utilization. In addition, substantial changes also take place in the physical and functional development of the immune system and intestinal microbial ecology. However, the focus of the current review was on nutrition-related challenges and nutritional approaches to assist the chick during this highly demanding period.

Abstract

Because the intestine is the primary nutrient supply organ, early development of digestive function in newly hatched chick will enable it to better utilize nutrients, grow efficiently, and achieve the genetic potential of contemporary broilers. Published data on the growth and digestive function of the gastrointestinal tract in neonatal poultry were reviewed. Several potential strategies to improve digestive tract growth and function in newly hatched chick are available and the options include breeder nutrition, in ovo feeding, early access to feed and water, special pre-starter diets, judicious use of feed additives, and early programming.

Age-associated variation in the gut microbiota of chinstrap penguins (Pygoscelis antarctica) reveals differences in food metabolism

Age is known to affect the gut microbiota in various animals; however, this relationship is poorly understood in seabirds. We investigated the temporal succession of gut microbiota in captive chinstrap penguins of different ages using high-throughput sequencing. The gut microbiota exhibited a significant age succession pattern, reaching maturity in adults and then declining with increasing age. Only 15 amplicon sequence variants were shared among the gut microbiota in chinstrap penguins at all studied ages, and these contributed to most of the age-related variations in total gut microbiota. Co-occurrence networks found that these key bacteria belonged to the genera Acinetobacter, Clostridium sensu stricto, and Fusobacterium, and more species interactions were found within the same taxonomy. Functional prediction indicated that most of the metabolic functions were more abundant in the gut microbiota in adult chinstrap penguins, except for carbohydrate metabolism, which was significantly more abundant in older individuals.

Gut dysbiosis and age-related neurological diseases; an innovative approach for therapeutic interventions

The gut microbiota is a complex ecosystem of bacteria, fungi, and viruses that acts as a critical regulator in microbial, metabolic, and immune responses in the host organism. Imbalances in the gut microbiota, termed "dysbiosis," often induce aberrant immune responses, which in turn disrupt the local and systemic homeostasis of the host. Emerging evidence has highlighted the importance of gut microbiota in intestinal diseases, and more recently, in age-related central nervous systems diseases, for example, stroke and Alzheimer's disease. It is now generally recognized that gut microbiota significantly influences host behaviors and modulates the interaction between microbiota, gut, and brain, via the "microbiota-gut-brain axis." Several approaches have been utilized to reduce age-related dysbiosis in experimental models and in clinical studies. These include strategies to manipulate the microbiome via fecal microbiota transplantation, administration of prebiotics and probiotics, and dietary interventions. In this review, we explore both clinical and preclinical therapies for treating age-related dysbiosis.

Past, Present, and Future of Gastrointestinal Microbiota Research in Cats

The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.

Microbial Community and Short-Chain Fatty Acid Mapping in the Intestinal Tract of Quail

Simple Summary

Quail is an economically important type of poultry, valued for its high meat quality and abundant egg nutrition. It is also an important laboratory research animal, widely used in developmental biology and toxicology tests. Since the gut microbiota plays a vital role in the host’s growth and health, we investigated the microbiota inhabiting the duodenum, jejunum, ileum, cecum, and colorectum of quail in the present study, using 16S rRNA gene sequencing and qPCR. The concentrations of short-chain fatty acids (SCFAs) were evaluated using gas chromatography. We found that the microbiota in the cecum was different from other intestinal sections and the enriched inhabitants of SCFA-producing bacterial genera made cecum the core locations of SCFA production in quail. The results of this study will provide fundamental data for further quail microbiology and functional studies.

Abstract

Quail is raised throughout China for egg and meat production. To deeply understand the gastrointestinal microbial composition and metabolites of quail, the present study characterized the microbiota inhabiting five intestinal locations of eight-week-old quail using 16S rRNA gene sequencing and qPCR, and evaluated the concentrations of short-chain fatty acids (SCFAs) in each individual location using gas chromatography. The results showed that Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Deferribacteres were the five most abundant phyla in the intestinal tract of quail. Firmicutes was largely dominant (>95%) in the small intestine, whereas Bacteroidetes increased significantly in the cecum (19.19%) and colorectum (8.09%). At the genus level, Lactobacillus was predominant in almost all sections (>50%) except in the cecum (7.26%), where Megamonas, Faecalibacterium, and Bacteroides were dominant. qPCR data indicated that the population sizes of both the total bacteria and proportions of the Firmicutes, Bacteroidetes, and Bacteroides group increased going from the proximal toward the distal end of the intestine in quail. The SCFA-producing bacterial genera Bacteroides, Faecalibacterium, Alistipes, Blautia, Parabacteroides, and Clostridium were of higher richness in the cecum and colorectum, where, accordingly, more SCFAs were produced. These findings will be helpful for the future study of quail microbiology, as well as its relationship with productive performance and health.

Residues of antibiotics in milk: persistence and quality interference

The objective of this study was (i) to analyze antibiotic residues, two which were beta-lactam antibiotics, one tetracycline, and one quinolone in the milk of lactating animals; (ii) to evaluate the interference of the drug ceftiofur which is considered as discard-zero. The SNAPduo™ ST Plus kit was used to evaluate the presence of beta-lactam antibiotics and tetracyclines in natural milk. Medications based on penicillin, ceftiofur, enrofloxacin, and oxytetracycline were used. As expected, the milk from control animals and animals administered with enrofloxacin did not present antibiotic residue because it is not one of the classes detected by the SNAPduo™ ST Plus kit, and thus it was used to prove the efficiency of the test. Ceftiofur, known as a “discard-zero” antibiotic, tested positive for the SNAPduo™ ST Plus kit and the BetaStar Combo® “S” test. Chemical residues were detected in cow’s milk treated with different groups of antibiotics after the withdrawal time indicated in the package inserts of the medicines used.

The infant gut microbiome as a microbial organ influencing host well-being

Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut.

Influence of cecotrophy on fat metabolism mediated by caecal microorganisms in New Zealand white rabbits

Cecotrophy is a special behaviour of rabbits. Eating soft faeces can improve feed efficiency and maintain gut flora in rabbits. In our previous study, we found that fasting from soft faeces significantly reduced growth rate and total cholesterol (TC) in New Zealand white rabbits (NZW rabbits), thereby resulting in lower values for body weight and fat deposition in the soft faeces fasting group than in the control group. However, it has not been demonstrated whether cecotrophy by NZW rabbits can regulate lipid metabolism by changing the diversity of caecal microorganisms. In this study, thirty-six 28-day-old weaned NZW female rabbits were randomly divided into two groups (the soft faeces fasting group and the control group) and fed to 90 days. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their soft faeces. Then, the caecal contents of three rabbits from the soft faeces fasting group and three rabbits from the control group were collected for metagenomic sequencing. We found that the abundance of Bacteroides increased, while Ruminococcus decreased, compared with the control group after fasting from soft faeces. Relative abundance was depressed for genes related to metabolic pathways such as ascorbate and aldarate metabolism, riboflavin metabolism and bile secretion. Moreover, there was a general correlation between variation in microbial diversity and fat deposition. Bacteroides affects body weight and TC by participating in the riboflavin metabolism pathway. By investigating the effect of cecotrophy on caecal microorganisms of rabbits, we identified the key microorganisms that regulate the rapid growth performance of NZW rabbits, which may provide useful reference for the future research and development of microecological preparations for NZW rabbits.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Multiplex touchdown PCR assay to enhance specificity and sensitivity for concurrent detection of four foodborne pathogens in raw milk

AIMS

The aim of this study was to develop a multiplex touchdown PCR (multiplex TD-PCR) for rapid and simultaneous detection of four major foodborne pathogens to avoid mispriming and unwanted production during gene amplification. Touchdown PCR is the modified form of standard PCR, which enhances specificity, sensitivity.

METHODS AND RESULTS

For this reason, a multiplex TD-PCR assay with a pre-enrichment step was developed to detect four foodborne pathogens namely Escherichia coli O157:H7, Listeria monocytogenes, Staphylococcus aureus, and Salmonella enterica serovar Enteritidis in pure culture and raw milk samples. The results showed that this protocol can eliminate the unwanted band or reduce significantly. The detection sensitivity of the single and multiplex TD-PCR was one cell per ml in pure culture. Furthermore, the detection limit of multiplex TD-PCR was one cell per 25 ml for artificially contaminated raw milk. We obtained similar results for detection of aforementioned pathogens in raw milk, after comparing the multiplex TD-PCR method with the traditional culture, except in one or two samples.

CONCLUSIONS

Hence, the proposed multiplex TD-PCR method could be confirmed as an effective way for rapid optimization of PCR reactions to increase specificity, sensitivity during gene amplification.

SIGNIFICANCE AND IMPACT OF THE STUDY

Hence, due to its simplicity, cost-effectiveness and being time-saving, it seems that this method is reasonable and economical for rapid optimization of PCR reactions.

Structural shifts in the intestinal microbiota of rats treated with cyclosporine A after orthotropic liver transplantation

Understanding the effect of immunosuppressive agents on intestinal microbiota is important to reduce the mortality and morbidity from orthotopic liver transplantation (OLT). We investigated the relationship between the commonly used immunosuppressive agent cyclosporine A (CSA) and the intestinal microbial variation in an OLT model. The rat samples were divided as follows: (1) N group (normal control); (2) I group (isograft LT, Brown Norway [BN] rat to BN); (3) R group (allograft LT, Lewis to BN rat); and (4) CSA group (R group treated with CSA). The intestinal microbiota was assayed by denaturing gradient gel electrophoresis profiles and by using real-time polymerase chain reaction. The liver histopathology and the alanine/aspartate aminotransferase ratio after LT were both ameliorated by CSA. In the CSA group, the numbers of rDNA gene copies of Clostridium cluster I, Clostridium cluster XIV, and Enterobacteriaceae decreased, whereas those of Faecalibacterium prausnitzii increased compared with the R group. Cluster analysis indicated that the samples from the N, I, and CSA groups were clustered, whereas the other clusters contained the samples from the R group. Hence, CSA ameliorates hepatic graft injury and partially restores gut microbiota following LT, and these may benefit hepatic graft rejection.

Changes in the Microbial Community Diversity of Oil Exploitation

To systematically evaluate the ecological changes of an active offshore petroleum production system, the variation of microbial communities at several sites (virgin field, wellhead, storage tank) of an oil production facility in east China was investigated by sequencing the V3 to V4 regions of 16S ribosomal ribonucleic acid (rRNA) of microorganisms. In general, a decrease of microbial community richness and diversity in petroleum mining was observed, as measured by operational taxonomic unit (OTU) numbers, α (Chao1 and Shannon indices), and β (principal coordinate analysis) diversity. Microbial community structure was strongly affected by environmental factors at the phylum and genus levels. At the phylum level, virgin field and wellhead were dominated by Proteobacteria, while the storage tank had higher presence of Firmicutes (29.3-66.9%). Specifically, the wellhead displayed a lower presentence of Proteobacteria (48.6-53.4.0%) and a higher presence of Firmicutes (24.4-29.6%) than the virgin field. At the genus level, the predominant genera were Ochrobactrum and Acinetobacter in the virgin field, Lactococcus and Pseudomonas in the wellhead, and Prauseria and Bacillus in the storage tank. Our study revealed that the microbial community structure was strongly affected by the surrounding environmental factors, such as temperature, oxygen content, salinity, and pH, which could be altered because of the oil production. It was observed that the various microbiomes produced surfactants, transforming the biohazard and degrading hydro-carbon. Altering the microbiome growth condition by appropriate human intervention and taking advantage of natural microbial resources can further enhance oil recovery technology.

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations

The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson's correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.

Essential Oils as an Intervention Strategy to Reduce Campylobacter in Poultry Production: A Review

Campylobacter is a major foodborne pathogen and can be acquired through consumption of poultry products. With 1.3 million United States cases a year, the high prevalence of Campylobacter within the poultry gastrointestinal tract is a public health concern and thus a target for the development of intervention strategies. Increasing demand for antibiotic-free products has led to the promotion of various alternative pathogen control measures both at the farm and processing level. One such measure includes utilizing essential oils in both pre- and post-harvest settings. Essential oils are derived from plant-based extracts, and there are currently over 300 commercially available compounds. They have been proposed to control Campylobacter in the gastrointestinal tract of broilers. When used in concentrations low enough to not influence sensory characteristics, essential oils have also been proposed to decrease bacterial contamination of the poultry product during processing. This review explores the use of essential oils, particularly thymol, carvacrol, and cinnamaldehyde, and their role in reducing Campylobacter concentrations both pre- and post-harvest. This review also details the suggested mechanisms of action of essential oils on Campylobacter.

Effects of Multi-Strain Probiotics Combined with Gardeniae fructus on Intestinal Microbiota, Metabolites, and Morphology in Broilers

This study was conducted to investigate the effects of a multi-strain probiotic combined with Gardeniae fructus on the growth performance, intestinal microbiota composition and metabolites, and intestinal morphology of broiler chickens. The dietary treatments included the basal diet without any antimicrobials (C), the basal diet supplemented with 10 ppm avilamycin (A), the basal diet supplemented with 0.1% multi-strain probiotics powder containing Lactobacillus acidophilus LAP5, L. fermentum P2, L. casei L21, and Pediococcus acidophilus LS (1×107 CFU/g) (P), and the basal diet supplemented with a mixture of 0.1% multi-strain probiotics and 0.05% herbal medicine G. fructus (PH). The results showed no significant differences in growth performance across all groups. A denaturing gradient gel electrophoresis analysis indicated that the groups PH, P, and A exhibited an increase in the similarity coefficients of their intestinal microbial populations. The real-time polymerase chain reaction (PCR) analysis showed that the relative concentrations of Firmicutes and Lactobacillus in the cecum and Bifidobacterium spp. in the ileum were higher in the groups PH, P, and A than in group C, and the diet supplemented with multi-strain probiotics combined with G. fructus decreased the concentrations of cecal Escherichia spp. and Clostridium perfringens. The broilers fed with multi-strain probiotics combined with G. fructus showed a significant increase (P<0.05) in the cecal short-chain fatty acids (total SCFA, acetic acid, and butyric acid) compared to the other groups. The treatment with antibiotics, multi-strain probiotics, or multi-strain probiotics combined with G. fructus increased the villus height/crypt depth ratio in the ileum of broilers. In conclusion, the supplementation of multi-strain probiotics combined with G. fructus was beneficial to the intestinal microflora composition, metabolites, and morphology in broilers.

Effect of Daily Consumption of Orange Juice on the Levels of Blood Glucose, Lipids, and Gut Microbiota Metabolites: Controlled Clinical Trials

Ingestion of bioactive compounds, such as hesperidin and naringin, found in citrus fruits and orange juice, can improve the homeostasis of gut microbiota. A controlled clinical study with temporal series intergroup design with 10 apparently healthy women (28.5 ± 8.4 years, 24.1 ± 3.3 kg/m²) were evaluated after continuous consumption of commercial pasteurized orange juice for 2 months. Samples of blood serum and stool were collected at basal time and periodically during the experiment for biochemical and microbiology assays. Intestinal microbiota was evaluated for total anaerobic bacteria, Lactobacillus spp., Bifidobacterium spp., and Clostridium spp. An independent culture evaluation was performed using Denaturing Gradient Gel Electrophoresis (DGGE). The pH, ammonium (NH₄⁺), and short-chain fatty acids (SCFAs) were evaluated for microbial metabolism. The results showed that daily intake of orange juice did not change women's body composition, but improved blood biochemical parameters, such as low-density lipoprotein-cholesterol, glucose, and insulin sensitivity. Orange juice positively modulated the composition and metabolic activity of microbiota, increasing the population of fecal Bifidobacterium spp. and lactobacillus spp. Polymerase chain reaction-DGGE of microbiota showed similar composition of total bacteria, and microbial metabolism showed a reduction of ammonia and an increase of the production of SCFAs. These results suggested that a daily consumption of orange had a positive effect on the intestinal microbiota and metabolic biomarkers of young women, which may be an effective alternative for a healthy drink.

Physiological Effects of Dietary Amino Acids on Gut Health and Functions of Swine

Gut health has significant implications for swine overall health status and nutrient utilization, due to its various functions including digestion and absorption of nutrients, secretion of mucins and immunoglobulins, and selective barrier protection against harmful antigens and pathogens. Both the basic anatomical structure of the gut (such as epithelial cells) and its luminal microbiota play important roles for maintaining gut health and functions. The interactions between epithelial cells and luminal microbiota have significant impact on host nutrition and health through the metabolism of dietary components. Amino acids, which are major nutrients for pigs, are not only obligatory for maintaining the intestinal mucosal mass and integrity, but also for supporting the growth of microorganisms in the gut. Dietary amino acids are the major fuel of the small intestinal mucosa. Particularly, glutamate, glutamine, and aspartate are the major oxidative fuel of the intestine. Emerging evidence shows that arginine activates the mTOR signaling pathway in the small intestine. Utilization of glycine by the small intestinal mucosa to synthesize glutathione is a very important physiological pathway, and the role of glycine as a powerful cytoprotectant has also been recognized. The major end products of methionine and cysteine metabolism are glutathione, homocysteine and taurine, which play important roles in the intestinal immune and anti-oxidative responses. Threonine is highly utilized by the gut and is particularly important for mucin synthesis and maintenance of gut barrier integrity. Moreover, either a deficiency or an excess of dietary threonine can reduce the synthesis of intestinal mucosal proteins and mucins in young pigs. Various new functions of amino acids on gut health and functions have been discovered in recent years. Thus, this review is to provide some up-to-date knowledge for industry application of dietary amino acids in order to enhance swine gut health and functions, and also it is to provide a comprehensive reference for further scientific research in this regard.

Horizontal Plasmid Transfer by Transformation in Escherichia coli: Environmental Factors and Possible Mechanisms

Transformation is one mode of horizontal gene transfer (HGT) in bacteria, wherein extracellular naked DNA is taken up by cells that have developed genetic competence. Sensitivity to DNase, which degrades naked DNA, is the key to distinguishing transformation from the DNase-resistant HGT mechanisms. In general, Escherichia coli is not believed to be naturally transformable; it develops high competence only under artificial conditions, including exposure to high Ca2+ concentrations. However, E. coli can reportedly express modest competence under certain conditions that are feasible in natural environments outside laboratory. In addition, recent data suggest that environmental factors influence multiple routes of transformation. In this mini review, we (1) summarize our studies on transformation-based HGT using E. coli experimental systems and (2) discuss the possible occurrence of transformation via multiple mechanisms in the environment and its possible impact on the spread of antibiotic resistance genes.

The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review

The microbiome of the broiler chicken gastrointestinal tract (GIT) has been extensively studied, and it has been amply demonstrated that it plays an important role in the health of the host, as it has a positive impact on the immune system, the physiology of the GIT, and productivity. Also, the microbiota is involved in reducing and preventing colonization by enteric pathogens through the process of competitive exclusion and the production of bacteriostatic and bactericidal substances. The taxonomic composition of the microbiota is affected by different factors, such as the organ, the age of the animal, diet and the use of antimicrobials.

Different kinds of additives that regulate the microbial community in feed include probiotics (live microorganisms that when administered in adequate amounts confer a health benefit on the host), prebiotics (ingredients that stimulate increased beneficial microbial activity in the digestive system in order to improve the health of the host) and phytobiotics (primary or secondary components of plants that contain bioactive compounds that exert a positive effect on the growth and health of animals). Phages may potentially provide an integrated solution to modulate the intestinal microbiome of chicken intestines, as they reduce specific pathogenic microbial populations, permitting the proliferation of beneficial microbiota. Studies have shown that the use of cocktails of phages, especially in high concentrations and with short lapses of time between exposure to the bacteria and treatment with phages, optimize the reduction of Salmonella in chickens. Each of these technologies has demonstrable positive effects on the health of the host and the reduction of the pathogen load in controlled assays.

This paper presents a comprehensive summary of the role of the microbiota in the broiler chicken gastrointestinal tract, and discusses the usefulness of different strategies for its modulation to control pathogens, with a particular emphasis on bacteriophages.

A Review of Prebiotics Against Salmonella in Poultry: Current and Future Potential for Microbiome Research Applications

Prebiotics are typically fermentable feed additives that can directly or indirectly support a healthy intestinal microbiota. Prebiotics have gained increasing attention in the poultry industry as wariness toward antibiotic use has grown in the face of foodborne pathogen drug resistance. Their potential as feed additives to improve growth, promote beneficial gastrointestinal microbiota, and reduce human-associated pathogens, has been well documented. However, their mechanisms remain relatively unknown. Prebiotics increasing short chain fatty acid (SCFA) production in the cecum have long since been considered a potential source for pathogen reduction. It has been previously concluded that prebiotics can improve the safety of poultry products by promoting the overall health and well-being of the bird as well as provide for an intestinal environment that is unfavorable for foodborne pathogens such as Salmonella. To better understand the precise benefit conferred by several prebiotics, "omic" technologies have been suggested and utilized. The data acquired from emerging technologies of microbiomics and metabolomics may be able to generate a more comprehensive detailed understanding of the microbiota and metabolome in the poultry gastrointestinal tract. This understanding, in turn, may allow for improved administration and optimization of prebiotics to prevent foodborne illness as well as elucidate unknown mechanisms of prebiotic actions. This review explores the use of prebiotics in poultry, their impact on gut Salmonella populations, and how utilization of next-generation technologies can elucidate the underlying mechanisms of prebiotics as feed additives.

Quantitative assessment of individual populations within polymicrobial biofilms

Selecting appropriate tools providing reliable quantitative measures of individual populations in biofilms is critical as we now recognize their true polymicrobial and heterogeneous nature. Here, plate count, quantitative real-time polymerase chain reaction (q-PCR) and peptide nucleic acid probe-fluorescence in situ hybridization (PNA-FISH) were employed to quantitate cystic fibrosis multispecies biofilms. Growth of Pseudomonas aeruginosa, Inquilinus limosus and Dolosigranulum pigrum was assessed in dual- and triple-species consortia under oxygen and antibiotic stress. Quantification methods, that were previously optimized and validated in planktonic consortia, were not always in agreement when applied in multispecies biofilms. Discrepancies in culture and molecular outcomes were observed, particularly for triple-species consortia and antibiotic-stressed biofilms. Some differences were observed, such as the higher bacterial counts obtained by q-PCR and/or PNA-FISH (≤4 log₁₀ cells/cm²) compared to culture. But the discrepancies between PNA-FISH and q-PCR data (eg D. pigrum limited assessment by q-PCR) demonstrate the effect of biofilm heterogeneity in method’s reliability. As the heterogeneity in biofilms is a reflection of a myriad of variables, tailoring an accurate picture of communities´ changes is crucial. This work demonstrates that at least two, but preferentially three, quantification techniques are required to obtain reliable measures and take comprehensive analysis of polymicrobial biofilm-associated infections.

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.

Profiles of commensal and opportunistic bacteria in human milk from healthy donors in Taiwan

Recent studies indicate that milk from healthy mothers may harbor potential probiotics. Nonetheless, the distribution of bacterial profiles in human milk samples in Taiwan is not fully understood. Therefore, with the aim to address this question, in this study, milk samples were collected from 33 healthy mothers (D1 to D33) visiting our hospital during a 6-month period. The milk microbiota was analyzed by a molecular approach (Illumina MiSeq sequencing). The results indicate that the milk samples have a unique profile and patterns of bacterial abundance levels. Moreover, in colostrum and transitional-milk samples, we detected 154 and 127 bacterial species, respectively, and these sets shared 42.6% of the bacterial species. The most common bacterial species among all milk samples were Staphylococcus epidermidis, Streptococcus lactarius, and Staphylococcus hominis, suggesting that the skin contamination route plays an important role in the composition of the milk microbiota. Nevertheless, four Lactobacillus species, Lactobacillus helveticus, Lactobacillus iners, Lactobacillus zeae, and Lactobacillus gasseri, were present in only 7 samples (21% prevalence), and bifidobacterial species were quite rare taxa among the present samples. The Staphylococcus aureus was detected in a total of 15 samples (45% prevalence), suggesting that this species may be commonly present in milk samples. In conclusion, each milk sample revealed a unique profile and patterns of bacterial abundance levels, and our data do not support the idea that lactobacilli and bifidobacteria are common and abundant in modern milk samples. Because none of the donors of the milk samples showed mastitis or any discomfort during the sampling process or at follow-up inspection, the microbiota of these milk samples is not likely to negatively affect its host. This study provides new information on the proportions of commensal bacteria in human milk in Taiwan.

The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita)

The critically endangered Northern bald ibis (Geronticus eremita) is a migratory bird that became extinct in Europe centuries ago. Since 2014, the Northern bald ibis is subject to an intensive rehabilitation and conservation regime aiming to reintroduce the bird in its original distribution range in Central Europe and concurrently to maintain bird health and increase population size. Hitherto, virtually nothing is known about the microbial communities associated with the ibis species; an information pivotal for the veterinary management of these birds. Hence, the present study was conducted to provide a baseline description of the cultivable microbiota residing in the Northern bald ibis. Samples derived from the choana, trachea, crop and cloaca were examined employing a culturomic approach in order to identify microbes at each sampling site and to compare their frequency among age classes, seasonal appearances and rearing types. In total, 94 microbial species including 14 potentially new bacterial taxa were cultivated from the Northern bald ibis with 36, 58 and 59 bacterial species isolated from the choana, crop and cloaca, respectively. The microbiota of the Northern bald ibis was dominated by members of the phylum Firmicutes, followed by Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria, altogether phylotypes commonly observed within avian gut environments. Differences in relative abundances of various microbial taxa were evident among sample types indicating mucosa-specific colonisation properties and tissue tropism. Besides, results of the present study indicate that the composition of microbiota was also affected by age, season (environment) and rearing type. While the prevalence of traditional pathogenic microbial species was extremely low, several opportunists including Clostridium perfringens toxotype A were frequently present in samples indicating that the Northern bald ibis may represent an important animal reservoir for these pathogens. In summary, the presented study provides a first inventory of the cultivable microbiota residing in the critically endangered Northern bald ibis and represents a first step in a wider investigation of the ibis microbiome with the ultimate goal to contribute to the management and survival of this critically endangered bird.

Gut microbial balance and liver transplantation: alteration, management, and prediction

Liver transplantation is a conventional treatment for terminal stage liver diseases. However, several complications still hinder the survival rate. Intestinal barrier destruction is widely observed among patients receiving liver transplant and suffering from ischemia-reperfusion or rejection injuries because of the relationship between the intestine and the liver, both in anatomy and function. Importantly, the resulting alteration of gut microbiota aggravates graft dysfunctions during the process. This article reviews the research progress for gut microbial alterations and liver transplantation. Especially, this work also evaluates research on the management of gut microbial alteration and the prediction of possible injuries utilizing microbial alteration during liver transplantation. In addition, we propose possible directions for research on gut microbial alteration during liver transplantation and offer a hypothesis on the utilization of microbial alteration in liver transplantation. The aim is not only to predict perioperative injuries but also to function as a method of treatment or even inhibit the rejection of liver transplantation.