As readers know, I have been on a deep dive into the results reported by Lipkin etc, doing one post a day on each of their findings over the last two weeks. The goal was to find patterns of what will help correct the shift. Below are my limited findings — based on very very limited published knowledge about each of the bacteria species.
Besides using PubMed, I have also obtain a copy of the 5 volume set Bergey’s manual of systematic bacteriology seeking additional fragments of knowledge.
In our review we found several weaknesses in this study:
- Constipation-predominant irritable bowel syndrome(C-IBS) and plain IBS breakdowns should have been included. [See Parabacteroides Distasonis post]
- Male and Female breakdowns should have been included. [See Parabacteroides Distasonis post]
My working hypothesis on the bacteria shift is simple, keeping with Osler’s Principles and Practice of Medicine. There is a risk of over-interpreting this data trying to find answers.
- Undergrowth is due to insufficient food, possibly
- absorption of D-ribose is 88–100% in the small intestines
- Possibly Fucose
- Overgrowth is due to too much food, possibly
- Lactic Acid
The over or under production of food is likely cause by an “island of stability” of other bacteria. My hope is that while we are attempting to correct these bacteria that we destabilize this island and drift back to a normal situation. Everything is intertwained and cross-supported.
- “Most of B. vulgatus [High], B. fragilis [High], B. ovatus and P. distasonis [Low] produced bacteriocins.[Natural antibiotics against other bacteria]”. P.Distasonis appears to have a different bacteriocin profile — this the two high producers may be surpressing it.
It appears that we can classify almost all of the HIGH bacteria to consumers of two food: Lactic Acid or Xylan.
Producers of Lactic Acid
- Clostridium asparagiforme [HIGH] ” The organism produced acetate, lactate, and ethanol as the major products of glucose fermentation.” 
Consumers of Lactic Acid
High d-lactic acid is a known characteristic for CFS. This is why I say to avoid lactic acid producing probiotics like Lactobacillus Acidophilus.
“The phylogenetic relationships of these nine lactate-utilizing, butyrate-producing strains based on their 16S rRNA sequences are summarized in Table 1. Four strains (from three individuals) are related to E. hallii, two (from two individuals) are A. caccae, and three (from two individuals) are distantly related to Clostridium indolis.” Lactate-Utilizing Bacteria, Isolated from Human Feces, That Produce Butyrate as a Major Fermentation Product 
So bacteria that consume lactic acid are expected to be well fed and likely high. This is true for:
Consumers of Xylan
So if we have levels of Xylan, we would expect well fed and likely high. This is true for:
- Bacteroides Xylanisolvens [HIGH]
- Bacteroides fragilis’ [HIGH]
- Prevotella buccalis [HIGH]
“xylose increased the ileal butyric acid proportion, whereas arabinose increased the fecal butyric acid proportion. Moreover, chicory pectin increased the acetic acid proportion in both ileal digesta and feces.”
I am really disappointed by their report. They reported only on a subgroup and appear not to have attempted to include in their scope, bacteria families reported prior (as far back as 1998!)
- Pasteurellales [Order]
- Lachnospiraceae [Family],
- unclassified Bacillales[Family] and
- Faecalibacterium [Genus],
- Gemella [Genus],
- Dorea [Genus], and
- Haemophilus [Genus]
- Pasteurellales [Order]
- Clostridiaceae [Family]
- Clostridium [Genus],
- Pseudoflavonifractor [Genus],
- Anaerostipes [Genus]
- Coprobacillus [Genus]
These were not examined by them for some strange reason:
- Lactobacillus (low) 
- Bifidobacteria (low) 
- E.Coli (low) 
- Klebsiella/Enterobacter (High) 
- Enterococcus (High) 
- Akkermansia (Low)
- Firmicutes/Bacteroides ratio
These shifts have been repeatedly seen in uBiome and other lab results posted here. As a holder of a M.Sc. doing medical statistics — the design and approach appears very heavily suspect.