Review

Jump to: Other

14 pages, 753 KiB

Open AccessReview

The Contribution of the Intestinal Microbiota to the Celiac Disease Pathogenesis along with the Effectiveness of Probiotic Therapy

by Oxana Zolnikova, Natiya Dzhakhaya, Elena Bueverova, Alla Sedova, Anastasia Kurbatova, Kira Kryuchkova, Tatyana Butkova, Alexander Izotov, Ludmila Kulikova, Kseniya Yurku, Pavel Chekulaev and Victoria Zaborova

Microorganisms 2023, 11(12), 2848; https://doi.org/10.3390/microorganisms11122848 - 23 Nov 2023

Cited by 2 | Viewed by 1214

Abstract

The development of many human disorders, including celiac disease (CD), is thought to be influenced by the microbiota of the gastrointestinal tract and its metabolites, according to current research. This study’s goal was to provide a concise summary of the information on the [...] Read more.

The development of many human disorders, including celiac disease (CD), is thought to be influenced by the microbiota of the gastrointestinal tract and its metabolites, according to current research. This study’s goal was to provide a concise summary of the information on the contribution of the intestinal microbiota to the CD pathogenesis, which was actively addressed while examining the reported pathogenesis of celiac disease (CD). We assumed that a change in gluten tolerance is formed under the influence of a number of different factors, including genetic predisposition and environmental factors. In related investigations, researchers have paid increasing attention to the study of disturbances in the composition of the intestinal microbiota and its functional activity in CD. A key finding of our review is that the intestinal microbiota has gluten-degrading properties, which, in turn, may have a protective effect on the development of CD. The intestinal microbiota contributes to maintaining the integrity of the intestinal barrier, preventing the formation of a “leaky” intestine. On the contrary, a change in the composition of the microbiota can act as a significant link in the pathogenesis of gluten intolerance and exacerbate the course of the disease. The possibility of modulating the composition of the microbiota by prescribing probiotic preparations is being considered. The effectiveness of the use of probiotics containing Lactobacillus and Bifidobacterium bacteria in experimental and clinical studies as a preventive and therapeutic agent has been documented. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

20 pages, 1806 KiB

Open AccessReview

Gut Microbiota in Diagnosis, Therapy and Prognosis of Cholangiocarcinoma and Gallbladder Carcinoma—A Scoping Review

by Ann-Kathrin Lederer, Hannah Rasel, Eva Kohnert, Clemens Kreutz, Roman Huber, Mohamed Tarek Badr, Patricia K. E. Dellweg, Fabian Bartsch and Hauke Lang

Microorganisms 2023, 11(9), 2363; https://doi.org/10.3390/microorganisms11092363 - 21 Sep 2023

Cited by 1 | Viewed by 1563

Abstract

Cancers of the biliary tract are more common in Asia than in Europe, but are highly lethal due to delayed diagnosis and aggressive tumor biology. Since the biliary tract is in direct contact with the gut via the enterohepatic circulation, this suggests a [...] Read more.

Cancers of the biliary tract are more common in Asia than in Europe, but are highly lethal due to delayed diagnosis and aggressive tumor biology. Since the biliary tract is in direct contact with the gut via the enterohepatic circulation, this suggests a potential role of gut microbiota, but to date, the role of gut microbiota in biliary tract cancers has not been elucidated. This scoping review compiles recent data on the associations between the gut microbiota and diagnosis, progression and prognosis of biliary tract cancer patients. Systematic review of the literature yielded 154 results, of which 12 studies and one systematic review were eligible for evaluation. The analyses of microbiota diversity indices were inconsistent across the included studies. In-depth analyses revealed differences between gut microbiota of biliary tract cancer patients and healthy controls, but without a clear tendency towards particular species in the studies. Additionally, most of the studies showed methodological flaws, for example non-controlling of factors that affect gut microbiota. At the current stage, there is a lack of evidence to support a general utility of gut microbiota diagnostics in biliary tract cancers. Therefore, no recommendation can be made at this time to include gut microbiota analyses in the management of biliary tract cancer patients. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

21 pages, 912 KiB

Open AccessReview

Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome

by Silvia Saturio, Alejandra Rey, Anna Samarra, Maria Carmen Collado, Marta Suárez, Laura Mantecón, Gonzalo Solís, Miguel Gueimonde and Silvia Arboleya

Microorganisms 2023, 11(8), 1907; https://doi.org/10.3390/microorganisms11081907 - 27 Jul 2023

Viewed by 2101

Abstract

The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in [...] Read more.

The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in the intestine. Similarly to microbiota composition, the possession of antibiotic resistance genes is affected by different perinatal factors. Moreover, antibiotics are the most used drugs in early life, and the use of antibiotics in pediatrics covers a wide variety of possibilities and treatment options. The disruption in the early microbiota caused by antibiotics may be of great relevance, not just because it may limit colonization by beneficial microorganisms and increase that of potential pathogens, but also because it may increase the levels of antibiotic resistance genes. The increase in antibiotic-resistant microorganisms is one of the major public health threats that humanity has to face and, therefore, understanding the factors that determine the development of the resistome in early life is of relevance. Recent advancements in sequencing technologies have enabled the study of the microbiota and the resistome at unprecedent levels. These aspects are discussed in this review as well as some potential interventions aimed at reducing the possession of resistance genes. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

20 pages, 1872 KiB

Open AccessReview

Impact of Early Weaning on Development of the Swine Gut Microbiome

by Benoit St-Pierre, Jorge Yair Perez Palencia and Ryan S. Samuel

Microorganisms 2023, 11(7), 1753; https://doi.org/10.3390/microorganisms11071753 - 05 Jul 2023

Cited by 3 | Viewed by 2001

Abstract

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with [...] Read more.

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

15 pages, 1096 KiB

Open AccessReview

Maternal Nutritional Status and the Microbiome across the Pregnancy and the Post-Partum Period

by Katie M. Strobel, Sandra E. Juul and David Taylor Hendrixson

Microorganisms 2023, 11(6), 1569; https://doi.org/10.3390/microorganisms11061569 - 13 Jun 2023

Cited by 1 | Viewed by 2265

Abstract

Appropriate nutrition during pregnancy and the post-partum period is vital for both the mothers and their offspring. Both under- and over-nourished status may have important microbial implications on the maternal and infant gut microbiomes. Alterations in the microbiome can have implications for a [...] Read more.

Appropriate nutrition during pregnancy and the post-partum period is vital for both the mothers and their offspring. Both under- and over-nourished status may have important microbial implications on the maternal and infant gut microbiomes. Alterations in the microbiome can have implications for a person’s risk of obesity and metabolic diseases. In this review, we examine alterations in the maternal gut, vaginal, placental, and milk microbiomes in the context of pre-pregnancy BMI, gestational weight gain, body composition, gestational diabetes, and maternal diet. We also investigate how the infant gut microbiome may be altered by these different parameters. Many of the microbial changes seen in under- and over-nourished states in birthing parents may result in long-term implications for the health of offspring. Differences in diet appear to be a major driver of the maternal and subsequently milk and offspring microbiomes. Further prospective longitudinal cohort studies are needed to examine nutrition and the microbiome to better understand its implications. Additionally, trials involving dietary interventions in child-bearing age adults should be explored to improve the mother and child’s risks for metabolic diseases. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

19 pages, 745 KiB

Open AccessReview

by Lynne V. McFarland, Ellie J. C. Goldstein and Ravina Kullar

Microorganisms 2023, 11(6), 1534; https://doi.org/10.3390/microorganisms11061534 - 09 Jun 2023

Cited by 2 | Viewed by 1612

Abstract

Clostridioides difficile infections (CDIs) have decreased in the past years, but since 2021, some hospitals have reported an increase in CDI rates. CDI remains a global concern and has been identified as an urgent threat to healthcare. Although multiple treatment options are available, [...] Read more.

Clostridioides difficile infections (CDIs) have decreased in the past years, but since 2021, some hospitals have reported an increase in CDI rates. CDI remains a global concern and has been identified as an urgent threat to healthcare. Although multiple treatment options are available, prevention strategies are more limited. As CDI is an opportunistic infection that arises after the normally protective microbiome has been disrupted, preventive measures aimed at restoring the microbiome have been tested. Our aim is to update the present knowledge on these various preventive strategies published in the past five years (2018–2023) to guide clinicians and healthcare systems on how to best prevent CDI. A literature search was conducted using databases (PubMed, Google Scholar, and clinicaltrials.gov) for phase 2–3 clinical trials for the primary or secondary prevention of CDI and microbiome and probiotics. As the main factor for Clostridium difficile infections is the disruption of the normally protective intestinal microbiome, strategies aimed at restoring the microbiome seem most rational. Some strains of probiotics, the use of fecal microbial therapy, and live biotherapeutic products offer promise to fill this niche; although, more large randomized controlled trials are needed that document the shifts in the microbiome population. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Graphical abstract

15 pages, 740 KiB

Open AccessReview

Amino Acid-Derived Bacterial Metabolites in the Colorectal Luminal Fluid: Effects on Microbial Communication, Metabolism, Physiology, and Growth

by François Blachier

Microorganisms 2023, 11(5), 1317; https://doi.org/10.3390/microorganisms11051317 - 17 May 2023

Cited by 3 | Viewed by 1724

Abstract

Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply [...] Read more.

Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply nitrogenous material to this microbial population. The bacteria in the large intestine luminal fluid release amino acids from the available proteins, and amino acids are then used for bacterial protein synthesis, energy production, and in other various catabolic pathways. The resulting metabolic intermediaries and end products can then accumulate in the colorectal fluid, and their concentrations appear to depend on different parameters, including microbiota composition and metabolic activity, substrate availability, and the capacity of absorptive colonocytes to absorb these metabolites. The aim of the present review is to present how amino acid-derived bacterial metabolites can affect microbial communication between both commensal and pathogenic microorganisms, as well as their metabolism, physiology, and growth. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Graphical abstract

16 pages, 11083 KiB

Open AccessReview

Isolation and Cultivation of Human Gut Microorganisms: A Review

by Xuchun Wan, Qianqian Yang, Xiangfeng Wang, Yun Bai and Zhi Liu

Microorganisms 2023, 11(4), 1080; https://doi.org/10.3390/microorganisms11041080 - 20 Apr 2023

Cited by 5 | Viewed by 4594

Abstract

Microbial resources from the human gut may find use in various applications, such as empirical research on the microbiome, the development of probiotic products, and bacteriotherapy. Due to the development of “culturomics”, the number of pure bacterial cultures obtained from the human gut [...] Read more.

Microbial resources from the human gut may find use in various applications, such as empirical research on the microbiome, the development of probiotic products, and bacteriotherapy. Due to the development of “culturomics”, the number of pure bacterial cultures obtained from the human gut has significantly increased since 2012. However, there is still a considerable number of human gut microbes to be isolated and cultured. Thus, to improve the efficiency of obtaining microbial resources from the human gut, some constraints of the current methods, such as labor burden, culture condition, and microbial targetability, still need to be optimized. Here, we overview the general knowledge and recent development of culturomics for human gut microorganisms. Furthermore, we discuss the optimization of several parts of culturomics including sample collection, sample processing, isolation, and cultivation, which may improve the current strategies. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

19 pages, 583 KiB

Open AccessReview

Impact of Gut Microbiota on Host Aggression: Potential Applications for Therapeutic Interventions Early in Development

by Katsunaka Mikami, Natsuru Watanabe, Takumi Tochio, Keitaro Kimoto, Fumiaki Akama and Kenji Yamamoto

Microorganisms 2023, 11(4), 1008; https://doi.org/10.3390/microorganisms11041008 - 12 Apr 2023

Cited by 3 | Viewed by 2461

Abstract

Aggression in the animal kingdom is a necessary component of life; however, certain forms of aggression, especially in humans, are pathological behaviors that are detrimental to society. Animal models have been used to study a number of factors, including brain morphology, neuropeptides, alcohol [...] Read more.

Aggression in the animal kingdom is a necessary component of life; however, certain forms of aggression, especially in humans, are pathological behaviors that are detrimental to society. Animal models have been used to study a number of factors, including brain morphology, neuropeptides, alcohol consumption, and early life circumstances, to unravel the mechanisms underlying aggression. These animal models have shown validity as experimental models. Moreover, recent studies using mouse, dog, hamster, and drosophila models have indicated that aggression may be affected by the “microbiota–gut–brain axis.” Disturbing the gut microbiota of pregnant animals increases aggression in their offspring. In addition, behavioral analyses using germ-free mice have shown that manipulating the intestinal microbiota during early development suppresses aggression. These studies suggest that treating the host gut microbiota during early development is critical. However, few clinical studies have investigated gut-microbiota-targeted treatments with aggression as a primary endpoint. This review aims to clarify the effects of gut microbiota on aggression and discusses the therapeutic potential of regulating human aggression by intervening in gut microbiota. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

26 pages, 1424 KiB

Open AccessReview

The Survival of Psychobiotics in Fermented Food and the Gastrointestinal Tract: A Review

by Patrycja Cichońska, Ewa Kowalska and Małgorzata Ziarno

Microorganisms 2023, 11(4), 996; https://doi.org/10.3390/microorganisms11040996 - 11 Apr 2023

Cited by 1 | Viewed by 4351

Abstract

In recent years, scientists have been particularly interested in the gut–brain axis, as well as the impact of probiotics on the nervous system. This has led to the creation of the concept of psychobiotics. The present review describes the mechanisms of action of [...] Read more.

In recent years, scientists have been particularly interested in the gut–brain axis, as well as the impact of probiotics on the nervous system. This has led to the creation of the concept of psychobiotics. The present review describes the mechanisms of action of psychobiotics, their use in food products, and their viability and survival during gastrointestinal passage. Fermented foods have a high potential of delivering probiotic strains, including psychobiotic ones. However, it is important that the micro-organisms remain viable in concentrations ranging from about 10⁶ to 10⁹ CFU/mL during processing, storage, and digestion. Reports indicate that a wide variety of dairy and plant-based products can be effective carriers for psychobiotics. Nonetheless, bacterial viability is closely related to the type of food matrix and the micro-organism strain. Studies conducted in laboratory conditions have shown promising results in terms of the therapeutic properties and viability of probiotics. Because human research in this field is still limited, it is necessary to broaden our understanding of the survival of probiotic strains in the human digestive tract, their resistance to gastric and pancreatic enzymes, and their ability to colonize the microbiota. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

16 pages, 701 KiB

Open AccessReview

The Gut–Liver Axis in Pediatric Liver Health and Disease

by Stephanie L. Rager and Melody Y. Zeng

Microorganisms 2023, 11(3), 597; https://doi.org/10.3390/microorganisms11030597 - 27 Feb 2023

Cited by 3 | Viewed by 2416

Abstract

There has been growing interest in the complex host–microbe interactions within the human gut and the role these interactions play in systemic health and disease. As an essential metabolic organ, the liver is intimately coupled to the intestinal microbial environment via the portal [...] Read more.

There has been growing interest in the complex host–microbe interactions within the human gut and the role these interactions play in systemic health and disease. As an essential metabolic organ, the liver is intimately coupled to the intestinal microbial environment via the portal venous system. Our understanding of the gut–liver axis comes almost exclusively from studies of adults; the gut–liver axis in children, who have unique physiology and differing gut microbial communities, remains poorly understood. Here, we provide a comprehensive overview of common pediatric hepatobiliary conditions and recent studies exploring the contributions of the gut microbiota to these conditions or changes of the gut microbiota due to these conditions. We examine the current literature regarding the microbial alterations that take place in biliary atresia, pediatric non-alcoholic fatty liver disease, Wilson’s disease, cystic fibrosis, inflammatory bowel disease, and viral hepatitis. Finally, we propose potential therapeutic approaches involving modulation of the gut microbiota and the gut–liver axis to mitigate the progression of pediatric liver disease. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

Other

Jump to: Review

14 pages, 1529 KiB

Open AccessSystematic Review

The Gut Microbiome in the First One Thousand Days of Neurodevelopment: A Systematic Review from the Microbiome Perspective

by Nathalia F. Naspolini, Paulo A. Schüroff, Maria J. Figueiredo, Gabriela E. Sbardellotto, Frederico R. Ferreira, Daniel Fatori, Guilherme V. Polanczyk, Alline C. Campos and Carla R. Taddei

Microorganisms 2024, 12(3), 424; https://doi.org/10.3390/microorganisms12030424 - 20 Feb 2024

Viewed by 2168

Abstract

Evidence shows that the gut microbiome in early life is an essential modulator of physiological processes related to healthy brain development, as well as mental and neurodegenerative disorders. Here, we conduct a systematic review of gut microbiome assessments on infants (both healthy and [...] Read more.

Evidence shows that the gut microbiome in early life is an essential modulator of physiological processes related to healthy brain development, as well as mental and neurodegenerative disorders. Here, we conduct a systematic review of gut microbiome assessments on infants (both healthy and with conditions that affect brain development) during the first thousand days of life, associated with neurodevelopmental outcomes, with the aim of investigating key microbiome players and mechanisms through which the gut microbiome affects the brain. Bacteroides and Bifidobacterium were associated with non-social fear behavior, duration of orientation, cognitive and motricity development, and neurotypical brain development. Lachnospiraceae, Streptococcus, and Faecalibacterium showed variable levels of influence on behavior and brain development. Few studies described mechanistic insights related to NAD salvage, aspartate and asparagine biosynthesis, methanogenesis, pathways involved in bile acid transformation, short-chain fatty acids production, and microbial virulence genes. Further studies associating species to gene pathways and robustness in data analysis and integration are required to elucidate the functional mechanisms underlying the role of microbiome–gut–brain axis in early brain development. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

22 pages, 5447 KiB

Open AccessSystematic Review

The Role of Carbohydrate Intake on the Gut Microbiome: A Weight of Evidence Systematic Review

by Lorena P. Mora-Flores, Rubén Moreno-Terrazas Casildo, José Fuentes-Cabrera, Hugo Alexer Pérez-Vicente, Guillermo de Anda-Jáuregui and Elier Ekberg Neri-Torres

Microorganisms 2023, 11(7), 1728; https://doi.org/10.3390/microorganisms11071728 - 30 Jun 2023

Cited by 4 | Viewed by 3585

Abstract

(1) Background: Carbohydrates are the most important source of nutritional energy for the human body. Carbohydrate digestion, metabolism, and their role in the gut microbiota modulation are the focus of multiple studies. The objective of this weight of evidence systematic review is to [...] Read more.

(1) Background: Carbohydrates are the most important source of nutritional energy for the human body. Carbohydrate digestion, metabolism, and their role in the gut microbiota modulation are the focus of multiple studies. The objective of this weight of evidence systematic review is to investigate the potential relationship between ingested carbohydrates and the gut microbiota composition at different taxonomic levels. (2) Methods: Weight of evidence and information value techniques were used to evaluate the relationship between dietary carbohydrates and the relative abundance of different bacterial taxa in the gut microbiota. (3) Results: The obtained results show that the types of carbohydrates that have a high information value are: soluble fiber with Bacteroides increase, insoluble fiber with Bacteroides and Actinobacteria increase, and Firmicutes decrease. Oligosaccharides with Lactobacillus increase and Enterococcus decrease. Gelatinized starches with Prevotella increase. Starches and resistant starches with Blautia decrease and Firmicutes increase. (4) Conclusions: This work provides, for the first time, an integrative review of the subject by using statistical techniques that have not been previously employed in microbiota reviews. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Latest Review Papers in Gut Microbiota 2023

Share This Special Issue

Special Issue Editor

Special Issue Information

Published Papers (13 papers)

Review

Other

Further Information

Guidelines

MDPI Initiatives

Follow MDPI