FEMS Microbiology Ecology

Cover image for Vol. 90 Issue 3

Gut Microbiome Virtual Issue

The history of human biology has been to look to the host and how it interacts with its environment to explain form and function. We are constantly exploring the interactions of the host’s genome with a variety of environmental factors to explain development and disease trends. This focus on the genome reached a pinnacle at the turn of the century when the first draft of the human genome was published and many claims followed this landmark event. However, in the proceeding decade many of these claims were not met and it became evident that host biology may not be simply due to our genomes. One of the main challenges to this view was that many rodents reared in a sterile environment did not develop correctly. Their immune systems were dysfunctional and many aspects of the host, such as the anatomy of the gut, were not the same as found in animals which were colonized by microbes. These observations coupled with the use of culture-independent methods started to re-direct our thinking into the realms of super-organism biology. In this new arena mammals were not just a product of their inherited genes interacting with the environment, but had co-evolved a requirement for functions that can only be provided by the microbiome that lives on and in them. Hence we are now at a new point in human biology, in which we are attempting to integrate the microbiome into how we function as complex organisms. This Virtual Issue of FEMS Microbiology Ecology explores researchers who are pioneering this new biological view and exploring how we can understand the ecology of the superorganism and its microbiome.

Julian R. Marchesi
School of Biosciences, Cardiff University

Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats
Stefanie Handl, Scot E. Dowd, Jose F. Garcia-Mazcorro, Jörg M. Steiner and Jan S. Suchodolski

Status of the phylogenetic diversity census of ruminal microbiomes
Minseok Kim, Mark Morrison and Zhongtang Yu

Establishment and development of intestinal microbiota in preterm neonates

Silvia Arboleya, Ana Binetti, Nuria Salazar, Nuria Fernández, Gonzalo Solís, Ana Hernández-Barranco, Abelardo Margolles, Clara G. de los Reyes-Gavilán and Miguel Gueimonde

Distal gut microbiota of adolescent children is different from that of adults
Richard Agans, Laura Rigsbee, Harshavardhan Kenche, Sonia Michail, Harry J. Khamis and Oleg Paliy

Predominant genera of fecal microbiota in children with atopic dermatitis are not altered by intake of probiotic bacteria Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bi-07
Nadja Larsen, Finn K. Vogensen, Rikke Gøbel, Kim F. Michaelsen, Waleed Abu Al-Soud, Søren J. Sørensen, Lars H. Hansen and Mogens Jakobsen

Phylogenetic characterization of bacteria in the gut of house flies (Musca domestica L.)
Arvind K. Gupta, Dana Nayduch, Pankaj Verma, Bhavin Shah, Hemant V. Ghate, Milind S. Patole and Yogesh S. Shouche

Midgut bacterial dynamics in Aedes aegypti
Olle Terenius, Jenny M. Lindh, Karolina Eriksson-Gonzales, Luc Bussière, Ane T. Laugen, Helen Bergquist, Kehmia Titanji and Ingrid Faye

Faecal microbiota in lean and obese dogs
Stefanie Handl, Alexander J. German, Shelley L. Holden, Scot E. Dowd, Jörg M. Steiner, Romy M. Heilmann, Ryan W. Grant, Kelly S. Swanson and Jan S. Suchodolski

Fecal microbial communities of healthy adult dogs fed raw meat-based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing
Alison N. Beloshapka, Scot E. Dowd, Jan S. Suchodolski, Jörg M. Steiner, Laura Duclos and Kelly S. Swanson

Daily follow-up of bacterial communities in the human gut reveals stable composition and host-specific patterns of interaction
Ana Durbán, Juan José Abellán, Nuria Jiménez-Hernández, Amparo Latorre and Andrés Moya

Diversity of the skin microbiota of fishes: evidence for host species specificity
Andrea Larsen, Zhen Tao, Stephen A. Bullard and Covadonga R. Arias

Diversity of human small intestinal Streptococcus and Veillonella populations
Bartholomeus van den Bogert, Oylum Erkus, Jos Boekhorst, Marcus de Goffau, Eddy J. Smid, Erwin G. Zoetendal and Michiel Kleerebezem

Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species
Rafael Muñoz-Tamayo, Béatrice Laroche, Éric Walter, Joël Doré, Sylvia H. Duncan, Harry J. Flint and Marion Leclerc

Monitoring horizontal antibiotic resistance gene transfer in a colonic fermentation model
Martina C. Haug, Sabine A. Tanner, Christophe Lacroix, Marc J.A. Stevens and Leo Meile

The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples
Johanna Maukonen, Catarina Simões and Maria Saarela

Germ-free status and altered caecal subdominant microbiota are associated with a high susceptibility to cow's milk allergy in mice
Bertrand Rodriguez, Guénolée Prioult, Rodrigo Bibiloni, Ioannis Nicolis, Annick Mercenier, Marie-José Butel and Anne-Judith Waligora-Dupriet

The intestinal microbiota in aged mice is modulated by dietary resistant starch and correlated with improvements in host responses
Sybille Tachon, June Zhou, Michael Keenan, Roy Martin and Maria L. Marco