Microbiota: From the Environment to Humans

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 33994

Special Issue Editors

Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, Università del Piemonte Orientale, 13100 Vercelli, Italy
Interests: soil microbiome; gut microbiome; metaproteome; holobiont
Special Issues, Collections and Topics in MDPI journals

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Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Viale San Pietro, 07100 Sassari, Italy
Interests: bacterial pathogenesis; cellular microbiology; metaproteomics; metagenomics; system microbiology

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Department of Sciences and Technological Innovation, University of Piemonte Orientale, viale T. Michel, 11-15121 Alessandria, Italy
Interests: soil microbial ecology; rhizosphere; plant–microbe interactions; PGPB
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Microbiota (referring to Bacteria, Archaea, Fungi, and viruses) are defined as the whole microbial communities associated to humans, animals, and plants, where each individual and its microbiota generate a holobiont. The homeostasis of the holobiont depends upon the host modulation of the microbiota populating the diverse surfaces and tissues. Most members of these microbial communities are not restricted to their holobionts and can be found in the microbiota of terrestrial and marine environments and in foods. The interaction between the host and its associated microbiota is so intimate as to determine its state of health or disease. Furthermore, the outcome of this dynamic balance is continuously influenced by the surrounding environment.

Microbiomes are the genomes associated to these microbial communities, and the metaproteome is the whole proteome expressed by these genomes. Thanks to the “omic” technologies, it is now possible to investigate both the genetic traits and the biological functions expressed by these complex microbial systems. Although the relationship between the host’s characteristics and its associated microbial communities has been extensively studied, the effects of one on the other are largely unknown.

The aim of this Special Issue is to provide an overview of the significance of microbial community fluxes from natural and built environments to humans, microbial community fluxes across foods, the effects of microbiota on host biology, and the integrated functions operating inside the holobiont.

Dr. Elisa Bona
Prof. Dr. Sergio Uzzau
Dr. Elisa Gamalero
Guest Editors

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Keywords

  • microbial community
  • holobiont
  • environment
  • food
  • metagenome
  • metaproteome

Published Papers (9 papers)

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Research

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16 pages, 2137 KiB  
Article
Influence of Sex on the Microbiota of the Human Face
by Clémence Robert, Federica Cascella, Marta Mellai, Nadia Barizzone, Flavio Mignone, Nadia Massa, Vincenzo Nobile and Elisa Bona
Microorganisms 2022, 10(12), 2470; https://doi.org/10.3390/microorganisms10122470 - 14 Dec 2022
Cited by 7 | Viewed by 2312
Abstract
The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, [...] Read more.
The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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13 pages, 2662 KiB  
Article
Intestinal Microbial Diversity of Free-Range and Captive Yak in Qinghai Province
by Ying Wen, Shaofei Li, Zishuo Wang, Hao Feng, Xiaoting Yao, Mingjie Liu, Jianjun Chang, Xiaoyu Ding, Huiying Zhao and Wentao Ma
Microorganisms 2022, 10(4), 754; https://doi.org/10.3390/microorganisms10040754 - 31 Mar 2022
Cited by 4 | Viewed by 2160
Abstract
Background: The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies [...] Read more.
Background: The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai–Tibet Plateau (QTP). Results: Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak. Conclusions: In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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16 pages, 1330 KiB  
Article
Microbiome Compositions and Resistome Levels after Antibiotic Treatment of Critically Ill Patients: An Observational Cohort Study
by Karen Leth Nielsen, Markus Harboe Olsen, Albert Pallejá, Søren Røddik Ebdrup, Nikolaj Sørensen, Oksana Lukjancenko, Rasmus L. Marvig, Kirsten Møller, Niels Frimodt-Møller and Frederik Boëtius Hertz
Microorganisms 2021, 9(12), 2542; https://doi.org/10.3390/microorganisms9122542 - 9 Dec 2021
Cited by 4 | Viewed by 2741
Abstract
Hospitalization and treatment with antibiotics increase the risk of acquiring multidrug-resistant bacteria due to antibiotic-mediated changes in patient microbiota. This study aimed to investigate how broad- and narrow-spectrum antibiotics affect the gut microbiome and the resistome in antibiotic naïve patients during neurointensive care. [...] Read more.
Hospitalization and treatment with antibiotics increase the risk of acquiring multidrug-resistant bacteria due to antibiotic-mediated changes in patient microbiota. This study aimed to investigate how broad- and narrow-spectrum antibiotics affect the gut microbiome and the resistome in antibiotic naïve patients during neurointensive care. Patients admitted to the neurointensive care unit were treated with broad-spectrum (meropenem or piperacillin/tazobactam) or narrow-spectrum antibiotic treatment (including ciprofloxacin, cefuroxime, vancomycin and dicloxacillin) according to clinical indications. A rectal swab was collected from each patient before and after 5–7 days of antibiotic therapy (N = 34), respectively. Shotgun metagenomic sequencing was performed and the composition of metagenomic species (MGS) was determined. The resistome was characterized with CARD RGI software and the CARD database. As a measure for selection pressure in the patient, we used the sum of the number of days with each antibiotic (antibiotic days). We observed a significant increase in richness and a tendency for an increase in the Shannon index after narrow-spectrum treatment. For broad-spectrum treatment the effect was more diverse, with some patients increasing and some decreasing in richness and Shannon index. This was studied further by comparison of patients who had gained or lost >10 MGS, respectively. Selection pressure was significantly higher in patients with decreased richness and a decreased Shannon index who received the broad treatment. A decrease in MGS richness was significantly correlated to the number of drugs administered and the selection pressure in the patient. Bray–Curtis dissimilarities were significant between the pre- and post-treatment of samples in the narrow group, indicating that the longer the narrow-spectrum treatment, the higher the differences between the pre- and the post-treatment microbial composition. We did not find significant differences between pre- and post-treatment for both antibiotic spectrum treatments; however, we observed that most of the antibiotic class resistance genes were higher in abundance in post-treatment after broad-spectrum treatment. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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25 pages, 27714 KiB  
Article
High Throughput Analysis Reveals Changes in Gut Microbiota and Specific Fecal Metabolomic Signature in Hematopoietic Stem Cell Transplant Patients
by Soumaya Kouidhi, Nessrine Souai, Oumaima Zidi, Amor Mosbah, Amel Lakhal, Tarek Ben Othmane, Dorra Belloumi, Farhat Ben Ayed, Elias Asimakis, Panagiota Stathopoulou, Ameur Cherif and George Tsiamis
Microorganisms 2021, 9(9), 1845; https://doi.org/10.3390/microorganisms9091845 - 31 Aug 2021
Cited by 4 | Viewed by 3104
Abstract
There is mounting evidence for the emerging role of gut microbiota (GM) and its metabolites in profoundly impacting allogenic hematopoietic stem cell transplantation (allo-HSCT) and its subsequent complications, mainly infections and graft versus host-disease (GvHD). The present study was performed in order to [...] Read more.
There is mounting evidence for the emerging role of gut microbiota (GM) and its metabolites in profoundly impacting allogenic hematopoietic stem cell transplantation (allo-HSCT) and its subsequent complications, mainly infections and graft versus host-disease (GvHD). The present study was performed in order to investigate changes in GM composition and fecal metabolic signature between transplant patients (n = 15) and healthy controls (n = 18). The intestinal microbiota was characterized by NGS and gas chromatography–mass spectrometry was employed to perform untargeted analysis of fecal metabolites. We found lower relative abundances of Actinobacteria, Firmicutes, and Bacteroidetes and a higher abundance of Proteobacteria phylum after allo-HSCT. Particularly, the GvHD microbiota was characterized by a lower relative abundance of the short-chain fatty acid-producing bacteria, namely, the Feacalibacterium, Akkermansia, and Veillonella genera and the Lachnospiraceae family, and an enrichment in multidrug-resistant bacteria belonging to Escherichia, Shigella, and Bacteroides. Moreover, network analysis showed that GvHD was linked to a higher number of positive interactions of Blautia and a significant mutual-exclusion rate of Citrobacter. The fecal metabolome was dominated by lipids in the transplant group when compared with the healthy individuals (p < 0.05). Overall, 76 metabolites were significantly altered within transplant recipients, of which 24 were selected as potential biomarkers. Furthermore, the most notable altered metabolic pathways included the TCA cycle; butanoate, propanoate, and pyruvate metabolisms; steroid biosynthesis; and glycolysis/gluconeogenesis. Specific biomarkers and altered metabolic pathways were correlated to GvHD onset. Our results showed significant shifts in gut microbiota structure and fecal metabolites characterizing allo-HSCT. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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17 pages, 2664 KiB  
Article
Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria
by Elisa Bona, Nadia Massa, Omrane Toumatia, Giorgia Novello, Patrizia Cesaro, Valeria Todeschini, Lara Boatti, Flavio Mignone, Houda Titouah, Abdelghani Zitouni, Guido Lingua, Francesco Vuolo and Elisa Gamalero
Microorganisms 2021, 9(7), 1359; https://doi.org/10.3390/microorganisms9071359 - 23 Jun 2021
Cited by 19 | Viewed by 3259
Abstract
Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, [...] Read more.
Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a “holobiont”. In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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11 pages, 3033 KiB  
Article
The Composition and Diversity of the Gut Microbiota in Children Is Modifiable by the Household Dogs: Impact of a Canine-Specific Probiotic
by Carlos Gómez-Gallego, Mira Forsgren, Marta Selma-Royo, Merja Nermes, Maria Carmen Collado, Seppo Salminen, Shea Beasley and Erika Isolauri
Microorganisms 2021, 9(3), 557; https://doi.org/10.3390/microorganisms9030557 - 8 Mar 2021
Cited by 10 | Viewed by 4517
Abstract
The development of the infant gut microbiota is initiated during pregnancy and continued through early life and childhood, guided by the immediate environment of the child. Our aim was to characterize the shared microbiota between dogs and children as well as to determine [...] Read more.
The development of the infant gut microbiota is initiated during pregnancy and continued through early life and childhood, guided by the immediate environment of the child. Our aim was to characterize the shared microbiota between dogs and children as well as to determine whether introduction to dogs of a dog-specific probiotic combination modifies the transfer process. We studied 31 children from allergic families with pet dog(s) and 18 control families without a dog. Altogether 37 dogs were randomized for a 4-week period in a double-blind design to receive canine-derived probiotic product containing a mixture of L. fermentum, L. plantarum, and L. rhamnosus, or placebo. Fecal samples from children and dogs were taken before and after the treatment. Distinctive gut microbiota composition was observed in children with dogs compared to those without a dog, characterized by higher abundance of Bacteroides and short-chain fatty acid producing bacteria such as Ruminococcus and Lachnospiraceae. Probiotic intervention in dogs had an impact on the composition of the gut microbiota in both dogs and children, characterized by a reduction in Bacteroides. We provide evidence for a direct effect of home environment and household pets on children microbiota and document that modification of dog microbiota by specific probiotics is reflected in children’s microbiota. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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Review

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22 pages, 5309 KiB  
Review
Microbiomics in Collusion with the Nervous System in Carcinogenesis: Diagnosis, Pathogenesis and Treatment
by Rodney Hull, Georgios Lolas, Stylianos Makrogkikas, Lasse D. Jensen, Konstantinos N. Syrigos, George Evangelou, Llewellyn Padayachy, Cyril Egbor, Ravi Mehrotra, Tshepiso Jan Makhafola, Meryl Oyomno and Zodwa Dlamini
Microorganisms 2021, 9(10), 2129; https://doi.org/10.3390/microorganisms9102129 - 11 Oct 2021
Cited by 3 | Viewed by 2560
Abstract
The influence of the naturally occurring population of microbes on various human diseases has been a topic of much recent interest. Not surprisingly, continuously growing attention is devoted to the existence of a gut brain axis, where the microbiota present in the gut [...] Read more.
The influence of the naturally occurring population of microbes on various human diseases has been a topic of much recent interest. Not surprisingly, continuously growing attention is devoted to the existence of a gut brain axis, where the microbiota present in the gut can affect the nervous system through the release of metabolites, stimulation of the immune system, changing the permeability of the blood–brain barrier or activating the vagus nerves. Many of the methods that stimulate the nervous system can also lead to the development of cancer by manipulating pathways associated with the hallmarks of cancer. Moreover, neurogenesis or the creation of new nervous tissue, is associated with the development and progression of cancer in a similar manner as the blood and lymphatic systems. Finally, microbes can secrete neurotransmitters, which can stimulate cancer growth and development. In this review we discuss the latest evidence that support the importance of microbiota and peripheral nerves in cancer development and dissemination. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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16 pages, 342 KiB  
Review
Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions
by Khalid J. Alzahrani
Microorganisms 2021, 9(10), 2021; https://doi.org/10.3390/microorganisms9102021 - 24 Sep 2021
Cited by 1 | Viewed by 2265
Abstract
In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific [...] Read more.
In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
18 pages, 1736 KiB  
Review
Recent Developments in the Study of Plant Microbiomes
by Bernard R. Glick and Elisa Gamalero
Microorganisms 2021, 9(7), 1533; https://doi.org/10.3390/microorganisms9071533 - 19 Jul 2021
Cited by 85 | Viewed by 8495
Abstract
To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia [...] Read more.
To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions. Full article
(This article belongs to the Special Issue Microbiota: From the Environment to Humans)
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